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JAL-3285 code changes to Jalview2XML not included in merge
author
tva
<tva@10.205.251.175>
Wed, 5 Jun 2019 13:33:02 +0000
(14:33 +0100)
committer
tva
<tva@10.205.251.175>
Wed, 5 Jun 2019 13:33:02 +0000
(14:33 +0100)
src/jalview/project/Jalview2XML.java
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diff --git
a/src/jalview/project/Jalview2XML.java
b/src/jalview/project/Jalview2XML.java
index
0ec8b97
..
d045a3c
100644
(file)
--- a/
src/jalview/project/Jalview2XML.java
+++ b/
src/jalview/project/Jalview2XML.java
@@
-1386,7
+1386,7
@@
public class Jalview2XML
jGroup.setTextCol2(sg.textColour2.getRGB());
jGroup.setTextColThreshold(sg.thresholdTextColour);
jGroup.setShowUnconserved(sg.getShowNonconserved());
jGroup.setTextCol2(sg.textColour2.getRGB());
jGroup.setTextColThreshold(sg.thresholdTextColour);
jGroup.setShowUnconserved(sg.getShowNonconserved());
- jGroup.setIgnoreGapsinConsensus(sg.isIgnoreGapsConsensus());
+ jGroup.setIgnoreGapsinConsensus(sg.getIgnoreGapsConsensus());
jGroup.setShowConsensusHistogram(sg.isShowConsensusHistogram());
jGroup.setShowSequenceLogo(sg.isShowSequenceLogo());
jGroup.setNormaliseSequenceLogo(sg.isNormaliseSequenceLogo());
jGroup.setShowConsensusHistogram(sg.isShowConsensusHistogram());
jGroup.setShowSequenceLogo(sg.isShowSequenceLogo());
jGroup.setNormaliseSequenceLogo(sg.isNormaliseSequenceLogo());
@@
-2124,8
+2124,9
@@
public class Jalview2XML
}
else if (!matchedFile.equals(pdbentry.getFile()))
{
}
else if (!matchedFile.equals(pdbentry.getFile()))
{
- warn("Probably lost some PDB-Sequence mappings for this structure file (which apparently has same PDB Entry code): "
- + pdbentry.getFile());
+ Cache.log.warn(
+ "Probably lost some PDB-Sequence mappings for this structure file (which apparently has same PDB Entry code): "
+ + pdbentry.getFile());
}
// record the
// file so we
}
// record the
// file so we
@@
-2625,7
+2626,7
@@
public class Jalview2XML
}
else
{
}
else
{
- debug("reusing DseqFor ID");
+ jalview.bin.Cache.log.debug("reusing DseqFor ID");
}
// mp.setMappingChoice(mpc);
}
// mp.setMappingChoice(mpc);
@@
-3542,7
+3543,7
@@
public class Jalview2XML
}
// adds feature to datasequence's feature set (since Jalview 2.10)
}
// adds feature to datasequence's feature set (since Jalview 2.10)
- alignmentSeq.addSequenceFeature(sf);
+ al.getSequenceAt(i).addSequenceFeature(sf);
}
}
if (vamsasSeqs.get(i).getDBRef().size() > 0)
}
}
if (vamsasSeqs.get(i).getDBRef().size() > 0)
@@
-3606,13
+3607,13
@@
public class Jalview2XML
.getStructureSelectionManager(Desktop.instance)
.registerPDBEntry(entry);
// adds PDBEntry to datasequence's set (since Jalview 2.10)
.getStructureSelectionManager(Desktop.instance)
.registerPDBEntry(entry);
// adds PDBEntry to datasequence's set (since Jalview 2.10)
- if (alignmentSeq.getDatasetSequence() != null)
+ if (al.getSequenceAt(i).getDatasetSequence() != null)
{
{
- alignmentSeq.getDatasetSequence().addPDBId(entry);
+ al.getSequenceAt(i).getDatasetSequence().addPDBId(entry);
}
else
{
}
else
{
- alignmentSeq.addPDBId(entry);
+ al.getSequenceAt(i).addPDBId(entry);
}
}
}
}
}
}
@@
-3620,10
+3621,10
@@
public class Jalview2XML
/*
* load any HMMER profile
*/
/*
* load any HMMER profile
*/
- String hmmJarFile = jseqs[i].getHmmerProfile();
+ String hmmJarFile = jseqs.get(i).getHmmerProfile();
if (hmmJarFile != null && jprovider != null)
{
if (hmmJarFile != null && jprovider != null)
{
- loadHmmerProfile(jprovider, hmmJarFile, alignmentSeq);
+ loadHmmerProfile(jprovider, hmmJarFile, al.getSequenceAt(i));
}
}
} // end !multipleview
}
}
} // end !multipleview
@@
-5508,7
+5509,10
@@
public class Jalview2XML
String id = object.getViewport().get(0).getSequenceSetId();
if (skipList.containsKey(id))
{
String id = object.getViewport().get(0).getSequenceSetId();
if (skipList.containsKey(id))
{
- debug("Skipping sequence set id " + id);
+ if (Cache.log != null && Cache.log.isDebugEnabled())
+ {
+ Cache.log.debug("Skipping seuqence set id " + id);
+ }
return true;
}
return false;
return true;
}
return false;
@@
-6149,7
+6153,7
@@
public class Jalview2XML
}
else
{
}
else
{
- debug("Ignoring " + jvobj.getClass() + " (ID = " + id);
+ Cache.log.debug("Ignoring " + jvobj.getClass() + " (ID = " + id);
}
}
}
}
}
}
@@
-6623,10
+6627,7
@@
public class Jalview2XML
maxcol = new Color(Integer.parseInt(colourModel.getRGB(), 16));
} catch (Exception e)
{
maxcol = new Color(Integer.parseInt(colourModel.getRGB(), 16));
} catch (Exception e)
{
- if (Cache.log != null)
- {
Cache.log.warn("Couldn't parse out graduated feature color.", e);
Cache.log.warn("Couldn't parse out graduated feature color.", e);
- }
}
NoValueColour noCol = colourModel.getNoValueColour();
}
NoValueColour noCol = colourModel.getNoValueColour();