From 83d955d73ec9236ce46af494fc4242909763bbc5 Mon Sep 17 00:00:00 2001 From: Jim Procter Date: Thu, 23 Jul 2015 18:49:16 +0100 Subject: [PATCH] JAL-1759 formatting --- src/jalview/gui/Jalview2XML.java | 131 ++++++++++++++++++-------------------- 1 file changed, 63 insertions(+), 68 deletions(-) diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java index be56292..91d6aa8 100644 --- a/src/jalview/gui/Jalview2XML.java +++ b/src/jalview/gui/Jalview2XML.java @@ -676,8 +676,7 @@ public class Jalview2XML { final SequenceI jds = jal.getSequenceAt(i); final SequenceI jdatasq = jds.getDatasetSequence() == null ? jds - : jds - .getDatasetSequence(); + : jds.getDatasetSequence(); String id = seqHash(jds); if (seqRefIds.get(id) != null) @@ -736,8 +735,7 @@ public class Jalview2XML if (jds.getSequenceFeatures() != null) { - jalview.datamodel.SequenceFeature[] sf = jds - .getSequenceFeatures(); + jalview.datamodel.SequenceFeature[] sf = jds.getSequenceFeatures(); int index = 0; while (index < sf.length) { @@ -900,36 +898,36 @@ public class Jalview2XML } } -// { -// AlcodonFrame alc = new AlcodonFrame(); -// vamsasSet.addAlcodonFrame(alc); -// for (int p = 0; p < acf.aaWidth; p++) -// { -// Alcodon cmap = new Alcodon(); -// if (acf.codons[p] != null) -// { -// // Null codons indicate a gapped column in the translated peptide -// // alignment. -// cmap.setPos1(acf.codons[p][0]); -// cmap.setPos2(acf.codons[p][1]); -// cmap.setPos3(acf.codons[p][2]); -// } -// alc.addAlcodon(cmap); -// } -// if (acf.getProtMappings() != null -// && acf.getProtMappings().length > 0) -// { -// SequenceI[] dnas = acf.getdnaSeqs(); -// jalview.datamodel.Mapping[] pmaps = acf.getProtMappings(); -// for (int m = 0; m < pmaps.length; m++) -// { -// AlcodMap alcmap = new AlcodMap(); -// alcmap.setDnasq(seqHash(dnas[m])); -// alcmap.setMapping(createVamsasMapping(pmaps[m], dnas[m], null, -// false)); -// alc.addAlcodMap(alcmap); -// } -// } + // { + // AlcodonFrame alc = new AlcodonFrame(); + // vamsasSet.addAlcodonFrame(alc); + // for (int p = 0; p < acf.aaWidth; p++) + // { + // Alcodon cmap = new Alcodon(); + // if (acf.codons[p] != null) + // { + // // Null codons indicate a gapped column in the translated peptide + // // alignment. + // cmap.setPos1(acf.codons[p][0]); + // cmap.setPos2(acf.codons[p][1]); + // cmap.setPos3(acf.codons[p][2]); + // } + // alc.addAlcodon(cmap); + // } + // if (acf.getProtMappings() != null + // && acf.getProtMappings().length > 0) + // { + // SequenceI[] dnas = acf.getdnaSeqs(); + // jalview.datamodel.Mapping[] pmaps = acf.getProtMappings(); + // for (int m = 0; m < pmaps.length; m++) + // { + // AlcodMap alcmap = new AlcodMap(); + // alcmap.setDnasq(seqHash(dnas[m])); + // alcmap.setMapping(createVamsasMapping(pmaps[m], dnas[m], null, + // false)); + // alc.addAlcodMap(alcmap); + // } + // } } } @@ -1032,13 +1030,11 @@ public class Jalview2XML if (sg.cs instanceof jalview.schemes.UserColourScheme) { - jGroup.setColour(setUserColourScheme(sg.cs, userColours, - jms)); + jGroup.setColour(setUserColourScheme(sg.cs, userColours, jms)); } else { - jGroup - .setColour(ColourSchemeProperty.getColourName(sg.cs)); + jGroup.setColour(ColourSchemeProperty.getColourName(sg.cs)); } } else if (sg.cs instanceof jalview.schemes.AnnotationColourGradient) @@ -1050,8 +1046,7 @@ public class Jalview2XML } else if (sg.cs instanceof jalview.schemes.UserColourScheme) { - jGroup - .setColour(setUserColourScheme(sg.cs, userColours, jms)); + jGroup.setColour(setUserColourScheme(sg.cs, userColours, jms)); } else { @@ -1211,8 +1206,8 @@ public class Jalview2XML else { setting.setColour(ap.getSeqPanel().seqCanvas - .getFeatureRenderer() - .getColour(renderOrder[ro]).getRGB()); + .getFeatureRenderer().getColour(renderOrder[ro]) + .getRGB()); } setting.setDisplay(av.getFeaturesDisplayed().isVisible( @@ -1420,8 +1415,7 @@ public class Jalview2XML { String varnaStateFile = varna.getStateInfo(model.rna); - jarEntryName = RNA_PREFIX + viewId + "_" - + nextCounter(); + jarEntryName = RNA_PREFIX + viewId + "_" + nextCounter(); copyFileToJar(jout, varnaStateFile, jarEntryName); rnaSessions.put(model, jarEntryName); } @@ -1604,8 +1598,8 @@ public class Jalview2XML private void storeAlignmentAnnotation(AlignmentAnnotation[] aa, IdentityHashMap groupRefs, - AlignmentViewport av, - Set calcIdSet, boolean storeDS, SequenceSet vamsasSet) + AlignmentViewport av, Set calcIdSet, boolean storeDS, + SequenceSet vamsasSet) { for (int i = 0; i < aa.length; i++) @@ -1635,9 +1629,11 @@ public class Jalview2XML if (groupIdr == null) { // make a locally unique String - groupRefs.put(annotation.groupRef, + groupRefs.put( + annotation.groupRef, groupIdr = ("" + System.currentTimeMillis() - + annotation.groupRef.getName() + groupRefs.size())); + + annotation.groupRef.getName() + groupRefs + .size())); } an.setGroupRef(groupIdr.toString()); } @@ -2415,7 +2411,8 @@ public class Jalview2XML .entrySet()) { AlignFrame af = candidate.getValue(); - if (!addedToSplitFrames.contains(af)) { + if (!addedToSplitFrames.contains(af)) + { Viewport view = candidate.getKey(); Desktop.addInternalFrame(af, view.getTitle(), view.getWidth(), view.getHeight()); @@ -2888,8 +2885,7 @@ public class Jalview2XML // set visiblity for other annotation in this view String annotationId = annotation.getId(); - if (annotationId != null - && annotationIds.containsKey(annotationId)) + if (annotationId != null && annotationIds.containsKey(annotationId)) { AlignmentAnnotation jda = annotationIds.get(annotationId); // in principle Visible should always be true for annotation displayed @@ -3123,8 +3119,7 @@ public class Jalview2XML SequenceGroup sg = new SequenceGroup(seqs, jGroup.getName(), cs, jGroup.getDisplayBoxes(), jGroup.getDisplayText(), - jGroup.getColourText(), jGroup.getStart(), - jGroup.getEnd()); + jGroup.getColourText(), jGroup.getStart(), jGroup.getEnd()); sg.setOutlineColour(new java.awt.Color(jGroup.getOutlineColour())); @@ -3163,8 +3158,8 @@ public class Jalview2XML if (jGroup.getId() != null && groupAnnotRefs.size() > 0) { // re-instate unique group/annotation row reference - List jaal = groupAnnotRefs - .get(jGroup.getId()); + List jaal = groupAnnotRefs.get(jGroup + .getId()); if (jaal != null) { for (AlignmentAnnotation jaa : jaal) @@ -3192,8 +3187,8 @@ public class Jalview2XML if (addAnnotSchemeGroup) { // reconstruct the annotation colourscheme - sg.cs = constructAnnotationColour( - jGroup.getAnnotationColours(), null, al, jms, false); + sg.cs = constructAnnotationColour(jGroup.getAnnotationColours(), + null, al, jms, false); } } } @@ -3325,8 +3320,8 @@ public class Jalview2XML for (int i = 0; i < jseq.getRnaViewerCount(); i++) { RnaViewer viewer = jseq.getRnaViewer(i); - AppVarna appVarna = findOrCreateVarnaViewer(viewer, uniqueSetSuffix, - ap); + AppVarna appVarna = findOrCreateVarnaViewer(viewer, + uniqueSetSuffix, ap); for (int j = 0; j < viewer.getSecondaryStructureCount(); j++) { @@ -3388,8 +3383,8 @@ public class Jalview2XML * viewer not found - make it */ RnaViewerModel model = new RnaViewerModel(postLoadId, - viewer.getTitle(), viewer.getXpos(), - viewer.getYpos(), viewer.getWidth(), viewer.getHeight(), + viewer.getTitle(), viewer.getXpos(), viewer.getYpos(), + viewer.getWidth(), viewer.getHeight(), viewer.getDividerLocation()); AppVarna varna = new AppVarna(model, ap); @@ -3674,12 +3669,12 @@ public class Jalview2XML * @param af * @param jprovider */ - protected void createChimeraViewer(Entry viewerData, - AlignFrame af, + protected void createChimeraViewer( + Entry viewerData, AlignFrame af, jarInputStreamProvider jprovider) { StructureViewerModel data = viewerData.getValue(); - String chimeraSessionFile = data.getStateData(); + String chimeraSessionFile = data.getStateData(); /* * Copy Chimera session from jar entry "viewer_"+viewId to a temporary file @@ -3716,8 +3711,8 @@ public class Jalview2XML String newViewId = viewerData.getKey(); ChimeraViewFrame cvf = new ChimeraViewFrame(chimeraSessionFile, - af.alignPanel, pdbArray, - seqsArray, colourByChimera, colourBySequence, newViewId); + af.alignPanel, pdbArray, seqsArray, colourByChimera, + colourBySequence, newViewId); cvf.setSize(data.getWidth(), data.getHeight()); cvf.setLocation(data.getX(), data.getY()); } @@ -4412,7 +4407,7 @@ public class Jalview2XML } } af.setMenusFromViewport(af.viewport); - + // TODO: we don't need to do this if the viewport is aready visible. /* * Add the AlignFrame to the desktop (it may be 'gathered' later), unless it @@ -5317,7 +5312,7 @@ public class Jalview2XML } } } - + return result; } -- 1.7.10.2