[Biojava-dev] BioJava code freeze, modularization and action items for sub modules

Tue Aug 25 02:50:09 UTC 2009

Andreas Prlic wrote:

> >> Once the modules are in place it is a good moment to hand over the
> >> leadership of the sub-modules to the new module-project leaders. It will be
> >> up to the module-lead to take the modules into the direction that he/she
> >> feels important. I would like to take this opportunity to suggest a couple
> >> of people as module-leaders and propose some action items for the modules.
> >> Feel free to comment or make additional suggestions...
> >
> > Sign me up for help with maven configuration/reporting, unit testing, and
> > generics API matters if you wish.
>
> Excellent, I will come back to you on this :-)
>
> >>  - don;t break backwards compatibility
> >
> > Seems to me the last one will greatly hamper the rest of this effort.
> > The next version needs to be binary compatible with 1.7?
>
>
> What I mean is that we should try not to disrupt things as much as is
> reasonable. I am all for a pragmatic approach. While trying to be
> conservative I guess refactoring should be discussed on a case by case
> basis. To give an example: an area where I am supporting re-factoring
> is the blast parser. The package name is confusing and we probably
> need some code changes to expose more details of the parser. Are you
> thinking of any other situtations, where you think breaking backwards
> compatibility will be inevitable?

Ah yes, pragmatically backwards compatible with 1.7 is a better goal.

Maintaining binary compatibility is very difficult, and something we
haven't really done in the past.  Consider the following biojava 1.6.1 vs
biojava 1.7 clirr [1] report.

   michael

[1] http://clirr.sf.net

---
ERROR: 6004: org.biojava.bio.alignment.NeedlemanWunsch: Changed type of field CostMatrix from double[][] to int[][]
ERROR: 7005: org.biojava.bio.alignment.NeedlemanWunsch: Parameter 1 of 'public NeedlemanWunsch(double, double, double, double, double, org.biojava.bio.alignment.SubstitutionMatrix)' has changed its type to short
ERROR: 7005: org.biojava.bio.alignment.NeedlemanWunsch: Parameter 2 of 'public NeedlemanWunsch(double, double, double, double, double, org.biojava.bio.alignment.SubstitutionMatrix)' has changed its type to short
ERROR: 7005: org.biojava.bio.alignment.NeedlemanWunsch: Parameter 3 of 'public NeedlemanWunsch(double, double, double, double, double, org.biojava.bio.alignment.SubstitutionMatrix)' has changed its type to short
ERROR: 7005: org.biojava.bio.alignment.NeedlemanWunsch: Parameter 4 of 'public NeedlemanWunsch(double, double, double, double, double, org.biojava.bio.alignment.SubstitutionMatrix)' has changed its type to short
ERROR: 7005: org.biojava.bio.alignment.NeedlemanWunsch: Parameter 5 of 'public NeedlemanWunsch(double, double, double, double, double, org.biojava.bio.alignment.SubstitutionMatrix)' has changed its type to short
ERROR: 7006: org.biojava.bio.alignment.NeedlemanWunsch: Return type of method 'public double getDelete()' has been changed to short
ERROR: 7006: org.biojava.bio.alignment.NeedlemanWunsch: Return type of method 'public double getEditDistance()' has been changed to int
ERROR: 7006: org.biojava.bio.alignment.NeedlemanWunsch: Return type of method 'public double getGapExt()' has been changed to short
ERROR: 7006: org.biojava.bio.alignment.NeedlemanWunsch: Return type of method 'public double getInsert()' has been changed to short
ERROR: 7006: org.biojava.bio.alignment.NeedlemanWunsch: Return type of method 'public double getMatch()' has been changed to short
ERROR: 7006: org.biojava.bio.alignment.NeedlemanWunsch: Return type of method 'public double getReplace()' has been changed to short
ERROR: 7005: org.biojava.bio.alignment.NeedlemanWunsch: Parameter 1 of 'protected double min(double, double, double)' has changed its type to int
ERROR: 7005: org.biojava.bio.alignment.NeedlemanWunsch: Parameter 2 of 'protected double min(double, double, double)' has changed its type to int
ERROR: 7005: org.biojava.bio.alignment.NeedlemanWunsch: Parameter 3 of 'protected double min(double, double, double)' has changed its type to int
ERROR: 7006: org.biojava.bio.alignment.NeedlemanWunsch: Return type of method 'protected double min(double, double, double)' has been changed to int
ERROR: 7006: org.biojava.bio.alignment.NeedlemanWunsch: Return type of method 'public double pairwiseAlignment(org.biojava.bio.symbol.SymbolList, org.biojava.bio.symbol.SymbolList)' has been changed to int
ERROR: 7005: org.biojava.bio.alignment.NeedlemanWunsch: Parameter 1 of 'public java.lang.String printCostMatrix(double[][], char[], char[])' has changed its type to int[][]
ERROR: 7005: org.biojava.bio.alignment.NeedlemanWunsch: Parameter 1 of 'public void setDelete(double)' has changed its type to short
ERROR: 7005: org.biojava.bio.alignment.NeedlemanWunsch: Parameter 1 of 'public void setGapExt(double)' has changed its type to short
ERROR: 7005: org.biojava.bio.alignment.NeedlemanWunsch: Parameter 1 of 'public void setInsert(double)' has changed its type to short
ERROR: 7005: org.biojava.bio.alignment.NeedlemanWunsch: Parameter 1 of 'public void setMatch(double)' has changed its type to short
ERROR: 7005: org.biojava.bio.alignment.NeedlemanWunsch: Parameter 1 of 'public void setReplace(double)' has changed its type to short
ERROR: 7005: org.biojava.bio.alignment.SequenceAlignment: Parameter 11 of 'public java.lang.String formatOutput(java.lang.String, java.lang.String, java.lang.String[], java.lang.String, int, int, long, int, int, long, double, long)' has changed its type to int
ERROR: 7006: org.biojava.bio.alignment.SequenceAlignment: Return type of method 'public java.lang.String formatOutput(java.lang.String, java.lang.String, java.lang.String[], java.lang.String, int, int, long, int, int, long, double, long)' has been changed to java.lang.StringBuffer
ERROR: 7006: org.biojava.bio.alignment.SequenceAlignment: Return type of method 'public double pairwiseAlignment(org.biojava.bio.symbol.SymbolList, org.biojava.bio.symbol.SymbolList)' has been changed to int
ERROR: 7005: org.biojava.bio.alignment.SmithWaterman: Parameter 1 of 'public SmithWaterman(double, double, double, double, double, org.biojava.bio.alignment.SubstitutionMatrix)' has changed its type to short
ERROR: 7005: org.biojava.bio.alignment.SmithWaterman: Parameter 2 of 'public SmithWaterman(double, double, double, double, double, org.biojava.bio.alignment.SubstitutionMatrix)' has changed its type to short
ERROR: 7005: org.biojava.bio.alignment.SmithWaterman: Parameter 3 of 'public SmithWaterman(double, double, double, double, double, org.biojava.bio.alignment.SubstitutionMatrix)' has changed its type to short
ERROR: 7005: org.biojava.bio.alignment.SmithWaterman: Parameter 4 of 'public SmithWaterman(double, double, double, double, double, org.biojava.bio.alignment.SubstitutionMatrix)' has changed its type to short
ERROR: 7005: org.biojava.bio.alignment.SmithWaterman: Parameter 5 of 'public SmithWaterman(double, double, double, double, double, org.biojava.bio.alignment.SubstitutionMatrix)' has changed its type to short
ERROR: 7006: org.biojava.bio.alignment.SmithWaterman: Return type of method 'public double pairwiseAlignment(org.biojava.bio.symbol.SymbolList, org.biojava.bio.symbol.SymbolList)' has been changed to int
ERROR: 7005: org.biojava.bio.alignment.SmithWaterman: Parameter 1 of 'public void setDelete(double)' has changed its type to short
ERROR: 7005: org.biojava.bio.alignment.SmithWaterman: Parameter 1 of 'public void setGapExt(double)' has changed its type to short
ERROR: 7005: org.biojava.bio.alignment.SmithWaterman: Parameter 1 of 'public void setInsert(double)' has changed its type to short
ERROR: 7005: org.biojava.bio.alignment.SmithWaterman: Parameter 1 of 'public void setMatch(double)' has changed its type to short
ERROR: 7005: org.biojava.bio.alignment.SmithWaterman: Parameter 1 of 'public void setReplace(double)' has changed its type to short
ERROR: 6004: org.biojava.bio.alignment.SubstitutionMatrix: Changed type of field matrix from int[][] to short[][]
ERROR: 6004: org.biojava.bio.alignment.SubstitutionMatrix: Changed type of field max from int to short
ERROR: 6004: org.biojava.bio.alignment.SubstitutionMatrix: Changed type of field min from int to short
ERROR: 7005: org.biojava.bio.alignment.SubstitutionMatrix: Parameter 2 of 'public SubstitutionMatrix(org.biojava.bio.symbol.FiniteAlphabet, int, int)' has changed its type to short
ERROR: 7005: org.biojava.bio.alignment.SubstitutionMatrix: Parameter 3 of 'public SubstitutionMatrix(org.biojava.bio.symbol.FiniteAlphabet, int, int)' has changed its type to short
INFO: 7011: org.biojava.bio.alignment.SubstitutionMatrix: Method 'public SubstitutionMatrix(java.io.File)' has been added
ERROR: 7006: org.biojava.bio.alignment.SubstitutionMatrix: Return type of method 'public int getMax()' has been changed to short
ERROR: 7006: org.biojava.bio.alignment.SubstitutionMatrix: Return type of method 'public int getMin()' has been changed to short
INFO: 7011: org.biojava.bio.alignment.SubstitutionMatrix: Method 'public org.biojava.bio.alignment.SubstitutionMatrix getSubstitutionMatrix(java.io.BufferedReader)' has been added
ERROR: 7006: org.biojava.bio.alignment.SubstitutionMatrix: Return type of method 'public int getValueAt(org.biojava.bio.symbol.Symbol, org.biojava.bio.symbol.Symbol)' has been changed to short
ERROR: 7005: org.biojava.bio.alignment.SubstitutionMatrix: Parameter 1 of 'protected int[][] parseMatrix(java.lang.String)' has changed its type to java.lang.Object
ERROR: 7006: org.biojava.bio.alignment.SubstitutionMatrix: Return type of method 'protected int[][] parseMatrix(java.lang.String)' has been changed to short[][]
ERROR: 7009: org.biojava.bio.alignment.SubstitutionMatrix: Accessibility of method 'protected int[][] parseMatrix(java.lang.String)' has been decreased from protected to private
INFO: 7003: org.biojava.bio.dp.onehead.SmallCursor: Method 'public boolean canAdvance()' has been removed, but an inherited definition exists.
INFO: 7003: org.biojava.bio.dp.onehead.SmallCursor: Method 'public org.biojava.bio.symbol.Symbol currentRes()' has been removed, but an inherited definition exists.
INFO: 7003: org.biojava.bio.dp.onehead.SmallCursor: Method 'public org.biojava.bio.symbol.Symbol lastRes()' has been removed, but an inherited definition exists.
INFO: 7011: org.biojava.bio.gui.glyph.ArrowGlyph: Method 'public ArrowGlyph(java.awt.Paint, java.awt.Paint)' has been added
INFO: 7011: org.biojava.bio.gui.glyph.ArrowGlyph: Method 'public ArrowGlyph(java.awt.geom.Rectangle2D$Float, java.awt.Paint, java.awt.Paint)' has been added
INFO: 7011: org.biojava.bio.gui.glyph.ArrowGlyph: Method 'public java.awt.Paint getFillPaint()' has been added
INFO: 7011: org.biojava.bio.gui.glyph.ArrowGlyph: Method 'public java.awt.Paint getOuterPaint()' has been added
INFO: 7011: org.biojava.bio.gui.glyph.ArrowGlyph: Method 'public void setDirection(int)' has been added
INFO: 7011: org.biojava.bio.gui.glyph.ArrowGlyph: Method 'public void setFillPaint(java.awt.Paint)' has been added
INFO: 7011: org.biojava.bio.gui.glyph.ArrowGlyph: Method 'public void setOuterPaint(java.awt.Paint)' has been added
INFO: 7011: org.biojava.bio.gui.glyph.RectangleGlyph: Method 'public java.awt.Paint getPaint()' has been added
INFO: 7011: org.biojava.bio.gui.glyph.RectangleGlyph: Method 'public void setPaint(java.awt.Paint)' has been added
INFO: 7011: org.biojava.bio.gui.glyph.TurnGlyph: Method 'public java.awt.Paint getPaint()' has been added
INFO: 7011: org.biojava.bio.gui.glyph.TurnGlyph: Method 'public void setPaint(java.awt.Paint)' has been added
INFO: 6009: org.biojava.bio.gui.sequence.GlyphFeatureRenderer: Accessibility of field fList has been increased from private to protected
INFO: 6009: org.biojava.bio.gui.sequence.GlyphFeatureRenderer: Accessibility of field gList has been increased from private to protected
INFO: 7011: org.biojava.bio.gui.sequence.GlyphFeatureRenderer: Method 'public boolean containsFilter(org.biojava.bio.seq.FeatureFilter)' has been added
INFO: 7011: org.biojava.bio.gui.sequence.GlyphFeatureRenderer: Method 'public org.biojava.bio.seq.FeatureFilter getFeatureFilter(int)' has been added
INFO: 7011: org.biojava.bio.gui.sequence.GlyphFeatureRenderer: Method 'public org.biojava.bio.gui.glyph.Glyph getGlyphForFilter(org.biojava.bio.seq.FeatureFilter)' has been added
INFO: 7011: org.biojava.bio.gui.sequence.GlyphFeatureRenderer: Method 'public void removeFilterWithGlyph(org.biojava.bio.seq.FeatureFilter)' has been added
INFO: 7011: org.biojava.bio.gui.sequence.GlyphFeatureRenderer: Method 'public void setGlyphForFilter(org.biojava.bio.seq.FeatureFilter, org.biojava.bio.gui.glyph.Glyph)' has been added
INFO: 6009: org.biojava.bio.gui.sequence.SequencePanelWrapper: Accessibility of field seqPanels has been increased from private to protected
INFO: 7003: org.biojava.bio.program.sax.BlastLikeSAXParser: Method 'public void addPrefixMapping(java.lang.String, java.lang.String)' has been removed, but an inherited definition exists.
INFO: 7003: org.biojava.bio.program.sax.BlastLikeSAXParser: Method 'public org.xml.sax.ContentHandler getContentHandler()' has been removed, but an inherited definition exists.
INFO: 7003: org.biojava.bio.program.sax.BlastLikeSAXParser: Method 'public org.xml.sax.DTDHandler getDTDHandler()' has been removed, but an inherited definition exists.
INFO: 7003: org.biojava.bio.program.sax.BlastLikeSAXParser: Method 'public org.xml.sax.EntityResolver getEntityResolver()' has been removed, but an inherited definition exists.
INFO: 7003: org.biojava.bio.program.sax.BlastLikeSAXParser: Method 'public org.xml.sax.ErrorHandler getErrorHandler()' has been removed, but an inherited definition exists.
INFO: 7003: org.biojava.bio.program.sax.BlastLikeSAXParser: Method 'public boolean getFeature(java.lang.String)' has been removed, but an inherited definition exists.
INFO: 7003: org.biojava.bio.program.sax.BlastLikeSAXParser: Method 'public java.lang.String getNamespacePrefix()' has been removed, but an inherited definition exists.
INFO: 7003: org.biojava.bio.program.sax.BlastLikeSAXParser: Method 'public boolean getNamespacePrefixes()' has been removed, but an inherited definition exists.
INFO: 7003: org.biojava.bio.program.sax.BlastLikeSAXParser: Method 'public boolean getNamespaces()' has been removed, but an inherited definition exists.
INFO: 7003: org.biojava.bio.program.sax.BlastLikeSAXParser: Method 'public java.lang.Object getProperty(java.lang.String)' has been removed, but an inherited definition exists.
INFO: 7003: org.biojava.bio.program.sax.BlastLikeSAXParser: Method 'public java.lang.String getURIFromPrefix(java.lang.String)' has been removed, but an inherited definition exists.
INFO: 7003: org.biojava.bio.program.sax.BlastLikeSAXParser: Method 'public void parse(java.lang.String)' has been removed, but an inherited definition exists.
INFO: 7003: org.biojava.bio.program.sax.BlastLikeSAXParser: Method 'public java.lang.String prefix(java.lang.String)' has been removed, but an inherited definition exists.
INFO: 7003: org.biojava.bio.program.sax.BlastLikeSAXParser: Method 'public void setContentHandler(org.xml.sax.ContentHandler)' has been removed, but an inherited definition exists.
INFO: 7003: org.biojava.bio.program.sax.BlastLikeSAXParser: Method 'public void setDTDHandler(org.xml.sax.DTDHandler)' has been removed, but an inherited definition exists.
INFO: 7003: org.biojava.bio.program.sax.BlastLikeSAXParser: Method 'public void setEntityResolver(org.xml.sax.EntityResolver)' has been removed, but an inherited definition exists.
INFO: 7003: org.biojava.bio.program.sax.BlastLikeSAXParser: Method 'public void setErrorHandler(org.xml.sax.ErrorHandler)' has been removed, but an inherited definition exists.
INFO: 7003: org.biojava.bio.program.sax.BlastLikeSAXParser: Method 'public void setFeature(java.lang.String, boolean)' has been removed, but an inherited definition exists.
INFO: 7003: org.biojava.bio.program.sax.BlastLikeSAXParser: Method 'public void setNamespacePrefix(java.lang.String)' has been removed, but an inherited definition exists.
INFO: 7003: org.biojava.bio.program.sax.BlastLikeSAXParser: Method 'public void setProperty(java.lang.String, java.lang.Object)' has been removed, but an inherited definition exists.
INFO: 7003: org.biojava.bio.program.sax.ClustalWAlignmentSAXParser: Method 'public void addPrefixMapping(java.lang.String, java.lang.String)' has been removed, but an inherited definition exists.
INFO: 7003: org.biojava.bio.program.sax.ClustalWAlignmentSAXParser: Method 'public org.xml.sax.ContentHandler getContentHandler()' has been removed, but an inherited definition exists.
INFO: 7003: org.biojava.bio.program.sax.ClustalWAlignmentSAXParser: Method 'public org.xml.sax.DTDHandler getDTDHandler()' has been removed, but an inherited definition exists.
INFO: 7003: org.biojava.bio.program.sax.ClustalWAlignmentSAXParser: Method 'public org.xml.sax.EntityResolver getEntityResolver()' has been removed, but an inherited definition exists.
INFO: 7003: org.biojava.bio.program.sax.ClustalWAlignmentSAXParser: Method 'public org.xml.sax.ErrorHandler getErrorHandler()' has been removed, but an inherited definition exists.
INFO: 7003: org.biojava.bio.program.sax.ClustalWAlignmentSAXParser: Method 'public boolean getFeature(java.lang.String)' has been removed, but an inherited definition exists.
INFO: 7003: org.biojava.bio.program.sax.ClustalWAlignmentSAXParser: Method 'public java.lang.String getNamespacePrefix()' has been removed, but an inherited definition exists.
INFO: 7003: org.biojava.bio.program.sax.ClustalWAlignmentSAXParser: Method 'public boolean getNamespacePrefixes()' has been removed, but an inherited definition exists.
INFO: 7003: org.biojava.bio.program.sax.ClustalWAlignmentSAXParser: Method 'public boolean getNamespaces()' has been removed, but an inherited definition exists.
INFO: 7003: org.biojava.bio.program.sax.ClustalWAlignmentSAXParser: Method 'public java.lang.Object getProperty(java.lang.String)' has been removed, but an inherited definition exists.
INFO: 7003: org.biojava.bio.program.sax.ClustalWAlignmentSAXParser: Method 'public java.lang.String getURIFromPrefix(java.lang.String)' has been removed, but an inherited definition exists.
INFO: 7003: org.biojava.bio.program.sax.ClustalWAlignmentSAXParser: Method 'public void parse(java.lang.String)' has been removed, but an inherited definition exists.
INFO: 7003: org.biojava.bio.program.sax.ClustalWAlignmentSAXParser: Method 'public java.lang.String prefix(java.lang.String)' has been removed, but an inherited definition exists.
INFO: 7003: org.biojava.bio.program.sax.ClustalWAlignmentSAXParser: Method 'public void setContentHandler(org.xml.sax.ContentHandler)' has been removed, but an inherited definition exists.
INFO: 7003: org.biojava.bio.program.sax.ClustalWAlignmentSAXParser: Method 'public void setDTDHandler(org.xml.sax.DTDHandler)' has been removed, but an inherited definition exists.
INFO: 7003: org.biojava.bio.program.sax.ClustalWAlignmentSAXParser: Method 'public void setEntityResolver(org.xml.sax.EntityResolver)' has been removed, but an inherited definition exists.
INFO: 7003: org.biojava.bio.program.sax.ClustalWAlignmentSAXParser: Method 'public void setErrorHandler(org.xml.sax.ErrorHandler)' has been removed, but an inherited definition exists.
INFO: 7003: org.biojava.bio.program.sax.ClustalWAlignmentSAXParser: Method 'public void setFeature(java.lang.String, boolean)' has been removed, but an inherited definition exists.
INFO: 7003: org.biojava.bio.program.sax.ClustalWAlignmentSAXParser: Method 'public void setNamespacePrefix(java.lang.String)' has been removed, but an inherited definition exists.
INFO: 7003: org.biojava.bio.program.sax.ClustalWAlignmentSAXParser: Method 'public void setProperty(java.lang.String, java.lang.Object)' has been removed, but an inherited definition exists.
INFO: 7003: org.biojava.bio.program.sax.FastaSearchSAXParser: Method 'public void addPrefixMapping(java.lang.String, java.lang.String)' has been removed, but an inherited definition exists.
INFO: 7003: org.biojava.bio.program.sax.FastaSearchSAXParser: Method 'public org.xml.sax.ContentHandler getContentHandler()' has been removed, but an inherited definition exists.
INFO: 7003: org.biojava.bio.program.sax.FastaSearchSAXParser: Method 'public org.xml.sax.DTDHandler getDTDHandler()' has been removed, but an inherited definition exists.
INFO: 7003: org.biojava.bio.program.sax.FastaSearchSAXParser: Method 'public org.xml.sax.EntityResolver getEntityResolver()' has been removed, but an inherited definition exists.
INFO: 7003: org.biojava.bio.program.sax.FastaSearchSAXParser: Method 'public org.xml.sax.ErrorHandler getErrorHandler()' has been removed, but an inherited definition exists.
INFO: 7003: org.biojava.bio.program.sax.FastaSearchSAXParser: Method 'public boolean getFeature(java.lang.String)' has been removed, but an inherited definition exists.
INFO: 7003: org.biojava.bio.program.sax.FastaSearchSAXParser: Method 'public java.lang.String getNamespacePrefix()' has been removed, but an inherited definition exists.
INFO: 7003: org.biojava.bio.program.sax.FastaSearchSAXParser: Method 'public boolean getNamespacePrefixes()' has been removed, but an inherited definition exists.
INFO: 7003: org.biojava.bio.program.sax.FastaSearchSAXParser: Method 'public boolean getNamespaces()' has been removed, but an inherited definition exists.
INFO: 7003: org.biojava.bio.program.sax.FastaSearchSAXParser: Method 'public java.lang.Object getProperty(java.lang.String)' has been removed, but an inherited definition exists.
INFO: 7003: org.biojava.bio.program.sax.FastaSearchSAXParser: Method 'public java.lang.String getURIFromPrefix(java.lang.String)' has been removed, but an inherited definition exists.
INFO: 7003: org.biojava.bio.program.sax.FastaSearchSAXParser: Method 'public void parse(java.lang.String)' has been removed, but an inherited definition exists.
INFO: 7003: org.biojava.bio.program.sax.FastaSearchSAXParser: Method 'public java.lang.String prefix(java.lang.String)' has been removed, but an inherited definition exists.
INFO: 7003: org.biojava.bio.program.sax.FastaSearchSAXParser: Method 'public void setContentHandler(org.xml.sax.ContentHandler)' has been removed, but an inherited definition exists.
INFO: 7003: org.biojava.bio.program.sax.FastaSearchSAXParser: Method 'public void setDTDHandler(org.xml.sax.DTDHandler)' has been removed, but an inherited definition exists.
INFO: 7003: org.biojava.bio.program.sax.FastaSearchSAXParser: Method 'public void setEntityResolver(org.xml.sax.EntityResolver)' has been removed, but an inherited definition exists.
INFO: 7003: org.biojava.bio.program.sax.FastaSearchSAXParser: Method 'public void setErrorHandler(org.xml.sax.ErrorHandler)' has been removed, but an inherited definition exists.
INFO: 7003: org.biojava.bio.program.sax.FastaSearchSAXParser: Method 'public void setFeature(java.lang.String, boolean)' has been removed, but an inherited definition exists.
INFO: 7003: org.biojava.bio.program.sax.FastaSearchSAXParser: Method 'public void setNamespacePrefix(java.lang.String)' has been removed, but an inherited definition exists.
INFO: 7003: org.biojava.bio.program.sax.FastaSearchSAXParser: Method 'public void setProperty(java.lang.String, java.lang.Object)' has been removed, but an inherited definition exists.
INFO: 7003: org.biojava.bio.program.sax.FastaSequenceSAXParser: Method 'public void addPrefixMapping(java.lang.String, java.lang.String)' has been removed, but an inherited definition exists.
INFO: 7003: org.biojava.bio.program.sax.FastaSequenceSAXParser: Method 'public org.xml.sax.ContentHandler getContentHandler()' has been removed, but an inherited definition exists.
INFO: 7003: org.biojava.bio.program.sax.FastaSequenceSAXParser: Method 'public org.xml.sax.DTDHandler getDTDHandler()' has been removed, but an inherited definition exists.
INFO: 7003: org.biojava.bio.program.sax.FastaSequenceSAXParser: Method 'public org.xml.sax.EntityResolver getEntityResolver()' has been removed, but an inherited definition exists.
INFO: 7003: org.biojava.bio.program.sax.FastaSequenceSAXParser: Method 'public org.xml.sax.ErrorHandler getErrorHandler()' has been removed, but an inherited definition exists.
INFO: 7003: org.biojava.bio.program.sax.FastaSequenceSAXParser: Method 'public boolean getFeature(java.lang.String)' has been removed, but an inherited definition exists.
INFO: 7003: org.biojava.bio.program.sax.FastaSequenceSAXParser: Method 'public java.lang.String getNamespacePrefix()' has been removed, but an inherited definition exists.
INFO: 7003: org.biojava.bio.program.sax.FastaSequenceSAXParser: Method 'public boolean getNamespacePrefixes()' has been removed, but an inherited definition exists.
INFO: 7003: org.biojava.bio.program.sax.FastaSequenceSAXParser: Method 'public boolean getNamespaces()' has been removed, but an inherited definition exists.
INFO: 7003: org.biojava.bio.program.sax.FastaSequenceSAXParser: Method 'public java.lang.Object getProperty(java.lang.String)' has been removed, but an inherited definition exists.
INFO: 7003: org.biojava.bio.program.sax.FastaSequenceSAXParser: Method 'public java.lang.String getURIFromPrefix(java.lang.String)' has been removed, but an inherited definition exists.
INFO: 7003: org.biojava.bio.program.sax.FastaSequenceSAXParser: Method 'public void parse(java.lang.String)' has been removed, but an inherited definition exists.
INFO: 7003: org.biojava.bio.program.sax.FastaSequenceSAXParser: Method 'public java.lang.String prefix(java.lang.String)' has been removed, but an inherited definition exists.
INFO: 7003: org.biojava.bio.program.sax.FastaSequenceSAXParser: Method 'public void setContentHandler(org.xml.sax.ContentHandler)' has been removed, but an inherited definition exists.
INFO: 7003: org.biojava.bio.program.sax.FastaSequenceSAXParser: Method 'public void setDTDHandler(org.xml.sax.DTDHandler)' has been removed, but an inherited definition exists.
INFO: 7003: org.biojava.bio.program.sax.FastaSequenceSAXParser: Method 'public void setEntityResolver(org.xml.sax.EntityResolver)' has been removed, but an inherited definition exists.
INFO: 7003: org.biojava.bio.program.sax.FastaSequenceSAXParser: Method 'public void setErrorHandler(org.xml.sax.ErrorHandler)' has been removed, but an inherited definition exists.
INFO: 7003: org.biojava.bio.program.sax.FastaSequenceSAXParser: Method 'public void setFeature(java.lang.String, boolean)' has been removed, but an inherited definition exists.
INFO: 7003: org.biojava.bio.program.sax.FastaSequenceSAXParser: Method 'public void setNamespacePrefix(java.lang.String)' has been removed, but an inherited definition exists.
INFO: 7003: org.biojava.bio.program.sax.FastaSequenceSAXParser: Method 'public void setProperty(java.lang.String, java.lang.Object)' has been removed, but an inherited definition exists.
INFO: 7003: org.biojava.bio.program.sax.PdbSAXParser: Method 'public void addPrefixMapping(java.lang.String, java.lang.String)' has been removed, but an inherited definition exists.
INFO: 7003: org.biojava.bio.program.sax.PdbSAXParser: Method 'public org.xml.sax.ContentHandler getContentHandler()' has been removed, but an inherited definition exists.
INFO: 7003: org.biojava.bio.program.sax.PdbSAXParser: Method 'public org.xml.sax.DTDHandler getDTDHandler()' has been removed, but an inherited definition exists.
INFO: 7003: org.biojava.bio.program.sax.PdbSAXParser: Method 'public org.xml.sax.EntityResolver getEntityResolver()' has been removed, but an inherited definition exists.
INFO: 7003: org.biojava.bio.program.sax.PdbSAXParser: Method 'public org.xml.sax.ErrorHandler getErrorHandler()' has been removed, but an inherited definition exists.
INFO: 7003: org.biojava.bio.program.sax.PdbSAXParser: Method 'public boolean getFeature(java.lang.String)' has been removed, but an inherited definition exists.
INFO: 7003: org.biojava.bio.program.sax.PdbSAXParser: Method 'public java.lang.String getNamespacePrefix()' has been removed, but an inherited definition exists.
INFO: 7003: org.biojava.bio.program.sax.PdbSAXParser: Method 'public boolean getNamespacePrefixes()' has been removed, but an inherited definition exists.
INFO: 7003: org.biojava.bio.program.sax.PdbSAXParser: Method 'public boolean getNamespaces()' has been removed, but an inherited definition exists.
INFO: 7003: org.biojava.bio.program.sax.PdbSAXParser: Method 'public java.lang.Object getProperty(java.lang.String)' has been removed, but an inherited definition exists.
INFO: 7003: org.biojava.bio.program.sax.PdbSAXParser: Method 'public java.lang.String getURIFromPrefix(java.lang.String)' has been removed, but an inherited definition exists.
INFO: 7003: org.biojava.bio.program.sax.PdbSAXParser: Method 'public java.lang.String prefix(java.lang.String)' has been removed, but an inherited definition exists.
INFO: 7003: org.biojava.bio.program.sax.PdbSAXParser: Method 'public void setContentHandler(org.xml.sax.ContentHandler)' has been removed, but an inherited definition exists.
INFO: 7003: org.biojava.bio.program.sax.PdbSAXParser: Method 'public void setDTDHandler(org.xml.sax.DTDHandler)' has been removed, but an inherited definition exists.
INFO: 7003: org.biojava.bio.program.sax.PdbSAXParser: Method 'public void setEntityResolver(org.xml.sax.EntityResolver)' has been removed, but an inherited definition exists.
INFO: 7003: org.biojava.bio.program.sax.PdbSAXParser: Method 'public void setErrorHandler(org.xml.sax.ErrorHandler)' has been removed, but an inherited definition exists.
INFO: 7003: org.biojava.bio.program.sax.PdbSAXParser: Method 'public void setFeature(java.lang.String, boolean)' has been removed, but an inherited definition exists.
INFO: 7003: org.biojava.bio.program.sax.PdbSAXParser: Method 'public void setNamespacePrefix(java.lang.String)' has been removed, but an inherited definition exists.
INFO: 7003: org.biojava.bio.program.sax.PdbSAXParser: Method 'public void setProperty(java.lang.String, java.lang.Object)' has been removed, but an inherited definition exists.
INFO: 7003: org.biojava.bio.program.sax.SequenceAlignmentSAXParser: Method 'public void addPrefixMapping(java.lang.String, java.lang.String)' has been removed, but an inherited definition exists.
INFO: 7003: org.biojava.bio.program.sax.SequenceAlignmentSAXParser: Method 'public org.xml.sax.ContentHandler getContentHandler()' has been removed, but an inherited definition exists.
INFO: 7003: org.biojava.bio.program.sax.SequenceAlignmentSAXParser: Method 'public org.xml.sax.DTDHandler getDTDHandler()' has been removed, but an inherited definition exists.
INFO: 7003: org.biojava.bio.program.sax.SequenceAlignmentSAXParser: Method 'public org.xml.sax.EntityResolver getEntityResolver()' has been removed, but an inherited definition exists.
INFO: 7003: org.biojava.bio.program.sax.SequenceAlignmentSAXParser: Method 'public org.xml.sax.ErrorHandler getErrorHandler()' has been removed, but an inherited definition exists.
INFO: 7003: org.biojava.bio.program.sax.SequenceAlignmentSAXParser: Method 'public boolean getFeature(java.lang.String)' has been removed, but an inherited definition exists.
INFO: 7003: org.biojava.bio.program.sax.SequenceAlignmentSAXParser: Method 'public java.lang.String getNamespacePrefix()' has been removed, but an inherited definition exists.
INFO: 7003: org.biojava.bio.program.sax.SequenceAlignmentSAXParser: Method 'public boolean getNamespacePrefixes()' has been removed, but an inherited definition exists.
INFO: 7003: org.biojava.bio.program.sax.SequenceAlignmentSAXParser: Method 'public boolean getNamespaces()' has been removed, but an inherited definition exists.
INFO: 7003: org.biojava.bio.program.sax.SequenceAlignmentSAXParser: Method 'public java.lang.Object getProperty(java.lang.String)' has been removed, but an inherited definition exists.
INFO: 7003: org.biojava.bio.program.sax.SequenceAlignmentSAXParser: Method 'public java.lang.String getURIFromPrefix(java.lang.String)' has been removed, but an inherited definition exists.
INFO: 7003: org.biojava.bio.program.sax.SequenceAlignmentSAXParser: Method 'public void parse(java.lang.String)' has been removed, but an inherited definition exists.
INFO: 7003: org.biojava.bio.program.sax.SequenceAlignmentSAXParser: Method 'public java.lang.String prefix(java.lang.String)' has been removed, but an inherited definition exists.
INFO: 7003: org.biojava.bio.program.sax.SequenceAlignmentSAXParser: Method 'public void setContentHandler(org.xml.sax.ContentHandler)' has been removed, but an inherited definition exists.
INFO: 7003: org.biojava.bio.program.sax.SequenceAlignmentSAXParser: Method 'public void setDTDHandler(org.xml.sax.DTDHandler)' has been removed, but an inherited definition exists.
INFO: 7003: org.biojava.bio.program.sax.SequenceAlignmentSAXParser: Method 'public void setEntityResolver(org.xml.sax.EntityResolver)' has been removed, but an inherited definition exists.
INFO: 7003: org.biojava.bio.program.sax.SequenceAlignmentSAXParser: Method 'public void setErrorHandler(org.xml.sax.ErrorHandler)' has been removed, but an inherited definition exists.
INFO: 7003: org.biojava.bio.program.sax.SequenceAlignmentSAXParser: Method 'public void setFeature(java.lang.String, boolean)' has been removed, but an inherited definition exists.
INFO: 7003: org.biojava.bio.program.sax.SequenceAlignmentSAXParser: Method 'public void setNamespacePrefix(java.lang.String)' has been removed, but an inherited definition exists.
INFO: 7003: org.biojava.bio.program.sax.SequenceAlignmentSAXParser: Method 'public void setProperty(java.lang.String, java.lang.Object)' has been removed, but an inherited definition exists.