From c9150af4f9655e743ec53ec60ac5553f95e17636 Mon Sep 17 00:00:00 2001 From: tva Date: Wed, 5 Jun 2019 14:33:02 +0100 Subject: [PATCH] JAL-3285 code changes to Jalview2XML not included in merge --- src/jalview/project/Jalview2XML.java | 31 ++++++++++++++++--------------- 1 file changed, 16 insertions(+), 15 deletions(-) diff --git a/src/jalview/project/Jalview2XML.java b/src/jalview/project/Jalview2XML.java index 0ec8b97..d045a3c 100644 --- 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.setIgnoreGapsinConsensus(sg.isIgnoreGapsConsensus()); + jGroup.setIgnoreGapsinConsensus(sg.getIgnoreGapsConsensus()); 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())) { - 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 @@ -2625,7 +2626,7 @@ public class Jalview2XML } else { - debug("reusing DseqFor ID"); + jalview.bin.Cache.log.debug("reusing DseqFor ID"); } // mp.setMappingChoice(mpc); @@ -3542,7 +3543,7 @@ public class Jalview2XML } // 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) @@ -3606,13 +3607,13 @@ public class Jalview2XML .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 { - alignmentSeq.addPDBId(entry); + al.getSequenceAt(i).addPDBId(entry); } } } @@ -3620,10 +3621,10 @@ public class Jalview2XML /* * load any HMMER profile */ - String hmmJarFile = jseqs[i].getHmmerProfile(); + String hmmJarFile = jseqs.get(i).getHmmerProfile(); if (hmmJarFile != null && jprovider != null) { - loadHmmerProfile(jprovider, hmmJarFile, alignmentSeq); + loadHmmerProfile(jprovider, hmmJarFile, al.getSequenceAt(i)); } } } // end !multipleview @@ -5508,7 +5509,10 @@ public class Jalview2XML 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; @@ -6149,7 +6153,7 @@ public class Jalview2XML } 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) { - if (Cache.log != null) - { Cache.log.warn("Couldn't parse out graduated feature color.", e); - } } NoValueColour noCol = colourModel.getNoValueColour(); -- 1.7.10.2