X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fgui%2FJalview2XML.java;h=d652da2a5aec05c6abeda173a8c290f6019d2211;hb=92f2bdf5a7a89ceefe2bff76ca75414cf0fb633c;hp=69ba4823a760709530d24658515f0c85f238e0ac;hpb=995f4cc089fdac19fca20c2386794a482bd43a99;p=jalview.git diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java index 69ba482..d652da2 100755 --- a/src/jalview/gui/Jalview2XML.java +++ b/src/jalview/gui/Jalview2XML.java @@ -18,21 +18,27 @@ */ package jalview.gui; -import jalview.binding.*; - -import jalview.io.*; import jalview.schemes.*; +import jalview.gui.*; + import java.io.*; import java.net.*; import java.util.*; + import java.util.jar.*; import javax.swing.*; +import org.exolab.castor.xml.*; + +import jalview.schemabinding.version2.*; + + + /** * DOCUMENT ME! @@ -43,7 +49,7 @@ import javax.swing.*; public class Jalview2XML { // SAVES SEVERAL ALIGNEMENT WINDOWS TO SAME JARFILE - public static void SaveState(File statefile) + public void SaveState(File statefile) { long creation = System.currentTimeMillis(); JInternalFrame[] frames = Desktop.desktop.getAllFrames(); @@ -115,7 +121,7 @@ public class Jalview2XML } // USE THIS METHOD TO SAVE A SINGLE ALIGNMENT WINDOW - public static void SaveAlignment(AlignFrame af, String jarFile, + public void SaveAlignment(AlignFrame af, String jarFile, String fileName) { try @@ -147,7 +153,7 @@ public class Jalview2XML * @param jout DOCUMENT ME! * @param out DOCUMENT ME! */ - public static void SaveState(AlignFrame af, long timeStamp, + public void SaveState(AlignFrame af, long timeStamp, String fileName, JarOutputStream jout, PrintWriter out) { Vector seqids = new Vector(); @@ -156,7 +162,7 @@ public class Jalview2XML AlignViewport av = af.viewport; JalviewModel object = new JalviewModel(); - object.setVamsasModel(new VamsasModel()); + object.setVamsasModel(new jalview.schemabinding.version2.VamsasModel()); object.setCreationDate(new java.util.Date(timeStamp)); object.setVersion(jalview.bin.Cache.getProperty("VERSION")); @@ -182,6 +188,7 @@ public class Jalview2XML vamsasSeq.setId(id + ""); vamsasSeq.setName(jal.getSequenceAt(i).getName()); vamsasSeq.setSequence(jal.getSequenceAt(i).getSequence()); + vamsasSeq.setDescription(jal.getSequenceAt(i).getDescription()); jseq = new JSeq(); jseq.setStart(jal.getSequenceAt(i).getStart()); @@ -191,6 +198,58 @@ public class Jalview2XML jseq.setId(id); + if(jal.getSequenceAt(i).getDatasetSequence().getSequenceFeatures()!=null) + { + jalview.datamodel.SequenceFeature[] sf + = jal.getSequenceAt(i).getDatasetSequence().getSequenceFeatures(); + int index = 0; + while(index < sf.length) + { + Features features = new Features(); + + features.setBegin(sf[index].getBegin()); + features.setEnd(sf[index].getEnd()); + features.setDescription(sf[index].getDescription()); + features.setStatus(sf[index].getStatus()); + features.setType(sf[index].getType()); + features.setFeatureGroup(sf[index].getFeatureGroup()); + jseq.addFeatures(features); + index ++; + } + } + + if(jal.getSequenceAt(i).getDatasetSequence().getPDBId()!=null) + { + Enumeration en = jal.getSequenceAt(i).getDatasetSequence().getPDBId().elements(); + while(en.hasMoreElements()) + { + Pdbids pdb = new Pdbids(); + jalview.datamodel.PDBEntry entry + = (jalview.datamodel.PDBEntry)en.nextElement(); + + pdb.setId(entry.getId()); + pdb.setType(entry.getType()); + + if(entry.getProperty()!=null) + { + PdbentryItem item = new PdbentryItem(); + Hashtable properties = entry.getProperty(); + Enumeration en2 = properties.keys(); + while(en2.hasMoreElements()) + { + Property prop = new Property(); + String key = en2.nextElement().toString(); + prop.setName(key); + prop.setValue( properties.get(key).toString() ); + item.addProperty(prop); + } + pdb.addPdbentryItem(item); + } + + jseq.addPdbids(pdb); + } + } + jms.addJSeq(jseq); vamsasSet.addSequence(vamsasSeq); id++; @@ -221,8 +280,11 @@ public class Jalview2XML tree.setThreshold(tp.treeCanvas.threshold); tree.setFitToWindow(tp.fitToWindow.getState()); - tree.setFontSize(tp.treeCanvas.fontSize); + tree.setFontName(tp.getTreeFont().getName()); + tree.setFontSize(tp.getTreeFont().getSize()); + tree.setFontStyle(tp.getTreeFont().getStyle()); tree.setMarkUnlinked(tp.placeholdersMenu.getState()); + tree.setShowBootstrap(tp.bootstrapMenu.getState()); tree.setShowDistances(tp.distanceMenu.getState()); @@ -254,7 +316,22 @@ public class Jalview2XML Annotation an = new Annotation(); an.setDescription(aa[i].description); - an.setGraph(aa[i].isGraph); + if(aa[i].graph>0) + { + an.setGraph(true); + an.setGraphType(aa[i].graph); + if(aa[i].getThreshold()!=null) + { + ThresholdLine line = new ThresholdLine(); + line.setLabel(aa[i].getThreshold().label); + line.setValue(aa[i].getThreshold().value); + line.setColour(aa[i].getThreshold().colour.getRGB()); + an.setThresholdLine(line); + } + } + else + an.setGraph(false); + an.setLabel(aa[i].label); AnnotationElement ae; @@ -294,41 +371,44 @@ public class Jalview2XML groups[i].setStart(sg.getStartRes()); groups[i].setEnd(sg.getEndRes()); groups[i].setName(sg.getName()); - - if (sg.cs instanceof ConservationColourScheme) + if(sg.cs!=null) { - ConservationColourScheme ccs = (ConservationColourScheme) sg.cs; - groups[i].setConsThreshold(ccs.inc); + if (sg.cs.conservationApplied()) + { + groups[i].setConsThreshold(sg.cs.getConservationInc()); - if (ccs.cs instanceof jalview.schemes.UserColourScheme) + if (sg.cs instanceof jalview.schemes.UserColourScheme) + { + groups[i].setColour(SetUserColourScheme(sg.cs, + userColours, + jms)); + } + else + { + groups[i].setColour(ColourSchemeProperty.getColourName(sg. + cs)); + } + } + else if(sg.cs instanceof jalview.schemes.AnnotationColourGradient) { - groups[i].setColour(SetUserColourScheme(ccs.cs, userColours, - jms)); + groups[i].setColour( + ColourSchemeProperty.getColourName( + ( (jalview.schemes.AnnotationColourGradient) sg.cs).getBaseColour())); + } + else if (sg.cs instanceof jalview.schemes.UserColourScheme) + { + groups[i].setColour(SetUserColourScheme(sg.cs, userColours, + jms)); } else { - groups[i].setColour(ColourSchemeProperty.getColourName(sg.cs)); + groups[i].setColour(ColourSchemeProperty.getColourName( + sg.cs)); } - } - else if (sg.cs instanceof jalview.schemes.UserColourScheme) - { - groups[i].setColour(SetUserColourScheme(sg.cs, userColours, - jms)); - } - else - { - groups[i].setColour(ColourSchemeProperty.getColourName( - sg.cs)); + groups[i].setPidThreshold(sg.cs.getThreshold()); } - if (sg.cs instanceof ResidueColourScheme) - { - groups[i].setPidThreshold(((ResidueColourScheme) sg.cs).getThreshold()); - } - - - groups[i].setOutlineColour(sg.getOutlineColour().getRGB()); groups[i].setDisplayBoxes(sg.getDisplayBoxes()); groups[i].setDisplayText(sg.getDisplayText()); @@ -345,6 +425,7 @@ public class Jalview2XML jms.setJGroup(groups); } + ///////////SAVE VIEWPORT Viewport view = new Viewport(); view.setTitle(af.getTitle()); @@ -360,6 +441,26 @@ public class Jalview2XML view.setBgColour(SetUserColourScheme(av.getGlobalColourScheme(), userColours, jms)); } + else if(av.getGlobalColourScheme() instanceof jalview.schemes.AnnotationColourGradient) + { + jalview.schemes.AnnotationColourGradient acg + = (jalview.schemes.AnnotationColourGradient)av.getGlobalColourScheme(); + + AnnotationColours ac = new AnnotationColours(); + ac.setAboveThreshold(acg.getAboveThreshold()); + ac.setThreshold(acg.getAnnotationThreshold()); + ac.setAnnotation(acg.getAnnotation()); + if(acg.getBaseColour() instanceof jalview.schemes.UserColourScheme) + ac.setColourScheme(SetUserColourScheme(acg.getBaseColour(), + userColours, jms)); + else + ac.setColourScheme(ColourSchemeProperty.getColourName(acg.getBaseColour())); + + ac.setMaxColour(acg.getMaxColour().getRGB()); + ac.setMinColour(acg.getMinColour().getRGB()); + view.setAnnotationColours(ac); + view.setBgColour("AnnotationColourGradient"); + } else { view.setBgColour(ColourSchemeProperty.getColourName( @@ -368,17 +469,19 @@ public class Jalview2XML ColourSchemeI cs = av.getGlobalColourScheme(); - if (cs instanceof ConservationColourScheme) + if(cs!=null) { - ConservationColourScheme ccs = (ConservationColourScheme)cs; - view.setConsThreshold(ccs.inc); - if(ccs.cs instanceof jalview.schemes.UserColourScheme) - view.setBgColour(SetUserColourScheme(ccs.cs, userColours, jms)); - } + if (cs.conservationApplied()) + { + view.setConsThreshold(cs.getConservationInc()); + if (cs instanceof jalview.schemes.UserColourScheme) + view.setBgColour(SetUserColourScheme(cs, userColours, jms)); + } - if (cs instanceof ResidueColourScheme) - { - view.setPidThreshold(((ResidueColourScheme) cs).getThreshold()); + if (cs instanceof ResidueColourScheme) + { + view.setPidThreshold(cs.getThreshold()); + } } view.setConservationSelected(av.getConservationSelected()); @@ -391,15 +494,42 @@ public class Jalview2XML view.setShowBoxes(av.getShowBoxes()); view.setShowColourText(av.getColourText()); view.setShowConservation(av.showConservation); - view.setShowFullId(av.getShowFullId()); + view.setShowFullId(av.getShowJVSuffix()); view.setShowIdentity(av.showIdentity); view.setShowQuality(av.showQuality); view.setShowSequenceFeatures(av.showSequenceFeatures); view.setShowText(av.getShowText()); view.setWrapAlignment(av.getWrapAlignment()); + if(av.featuresDisplayed!=null) + { + jalview.schemabinding.version2.FeatureSettings fs + = new jalview.schemabinding.version2.FeatureSettings(); + + String [] renderOrder = + af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().renderOrder; + for(int ro=0; ro 0) + { + Features[] features = JSEQ[i].getFeatures(); + for (int f = 0; f < features.length; f++) + { + jalview.datamodel.SequenceFeature sf + = new jalview.datamodel.SequenceFeature(features[f].getType(), + features[f].getDescription(), features[f].getStatus(), + features[f].getBegin(), features[f].getEnd(), + features[f].getFeatureGroup()); + + al.getSequenceAt(i).getDatasetSequence().addSequenceFeature(sf); + } + } + if (JSEQ[i].getPdbidsCount() > 0) + { + Pdbids[] ids = JSEQ[i].getPdbids(); + for (int p = 0; p < ids.length; p++) + { + jalview.datamodel.PDBEntry entry = new jalview.datamodel.PDBEntry(); + entry.setId(ids[p].getId()); + entry.setType(ids[p].getType()); + al.getSequenceAt(i).getDatasetSequence().addPDBId(entry); + } + + } + } + + ///////////////////////////////// ////////////////////////////////// //LOAD ANNOTATIONS if (vamsasSet.getAnnotation() != null) @@ -587,7 +787,7 @@ public class Jalview2XML { anot[ae[aa].getPosition()] = new jalview.datamodel.Annotation(ae[aa].getDisplayCharacter(), ae[aa].getDescription(), - ae[aa].getSecondaryStructure().charAt(0), + ae[aa].getSecondaryStructure().length()==0?' ':ae[aa].getSecondaryStructure().charAt(0), ae[aa].getValue()); } @@ -595,8 +795,20 @@ public class Jalview2XML if (an[i].getGraph()) { - jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(), - an[i].getDescription(), anot, 0, 0, 1); + jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(), + an[i].getDescription(), anot, 0, 0, + an[i].getGraphType()); + + if (an[i].getThresholdLine() != null) + { + jaa.setThreshold(new jalview.datamodel.GraphLine( + an[i].getThresholdLine().getValue(), + an[i].getThresholdLine().getLabel(), + new java.awt.Color(an[i].getThresholdLine().getColour())) + ); + + } + } else { @@ -608,6 +820,7 @@ public class Jalview2XML } } + ///////////////////////////////// // LOAD VIEWPORT Viewport[] views = jms.getViewport(); @@ -615,6 +828,7 @@ public class Jalview2XML AlignFrame af = new AlignFrame(al); + // af.changeColour() ); ///////////////////////// //LOAD GROUPS @@ -638,10 +852,8 @@ public class Jalview2XML groups[i].getColour()); } - if (cs instanceof ResidueColourScheme) - { - ((ResidueColourScheme) cs).setThreshold(groups[i].getPidThreshold(), true); - } + if(cs!=null) + cs.setThreshold(groups[i].getPidThreshold(), true); } Vector seqs = new Vector(); @@ -668,20 +880,20 @@ public class Jalview2XML sg.getWidth() - 1); c.calculate(); c.verdict(false, 25); - cs = new ConservationColourScheme(c, cs); - sg.cs = cs; + sg.cs.setConservation(c); } al.addGroup(sg); } } - Desktop.addInternalFrame(af, view.getTitle(), - AlignFrame.NEW_WINDOW_WIDTH, AlignFrame.NEW_WINDOW_HEIGHT); + + af.setBounds(view.getXpos(), view.getYpos(), view.getWidth(), view.getHeight()); af.viewport.setStartRes(view.getStartRes()); af.viewport.setStartSeq(view.getStartSeq()); + af.viewport.setShowAnnotation(view.getShowAnnotation()); af.viewport.showConservation = view.getShowConservation(); af.viewport.showQuality = view.getShowQuality(); af.viewport.showIdentity = view.getShowIdentity(); @@ -692,8 +904,8 @@ public class Jalview2XML af.viewport.setConservationSelected(view.getConservationSelected()); af.conservationMenuItem.setSelected(view.getConservationSelected()); - af.viewport.setShowFullId(view.getShowFullId()); - af.fullSeqId.setSelected(view.getShowFullId()); + af.viewport.setShowJVSuffix(view.getShowFullId()); + af.seqLimits.setSelected(view.getShowFullId()); af.viewport.setFont(new java.awt.Font(view.getFontName(), view.getFontStyle(), view.getFontSize())); @@ -729,39 +941,149 @@ public class Jalview2XML { cs = GetUserColourScheme(jms, view.getBgColour()); } - else + else if(view.getBgColour().startsWith("Annotation")) { - cs = ColourSchemeProperty.getColour(al, view.getBgColour()); - } + //int find annotation + for (int i = 0; i < af.viewport.alignment.getAlignmentAnnotation().length; i++) + { + if (af.viewport.alignment.getAlignmentAnnotation()[i].label. + equals(view.getAnnotationColours().getAnnotation())) + { + if (af.viewport.alignment.getAlignmentAnnotation()[i]. + getThreshold() == null) + { + af.viewport.alignment.getAlignmentAnnotation()[i]. + setThreshold( + new jalview.datamodel.GraphLine( + view.getAnnotationColours().getThreshold(), + "Threshold", java.awt.Color.black) + + ); + } + + + if (view.getAnnotationColours().getColourScheme().equals( + "None")) + { + cs = new AnnotationColourGradient( + af.viewport.alignment.getAlignmentAnnotation()[i], + new java.awt.Color(view.getAnnotationColours(). + getMinColour()), + new java.awt.Color(view.getAnnotationColours(). + getMaxColour()), + view.getAnnotationColours().getAboveThreshold()); + } + else if (view.getAnnotationColours().getColourScheme(). + startsWith("ucs")) + { + cs = new AnnotationColourGradient( + af.viewport.alignment.getAlignmentAnnotation()[i], + GetUserColourScheme(jms, view.getAnnotationColours(). + getColourScheme()), + view.getAnnotationColours().getAboveThreshold() + ); + } + else + { + cs = new AnnotationColourGradient( + af.viewport.alignment.getAlignmentAnnotation()[i], + ColourSchemeProperty.getColour(al, + view.getAnnotationColours().getColourScheme()), + view.getAnnotationColours().getAboveThreshold() + ); + } + + // Also use these settings for all the groups + if (al.getGroups() != null) + for (int g = 0; g < al.getGroups().size(); g++) + { + jalview.datamodel.SequenceGroup sg + = (jalview.datamodel.SequenceGroup)al.getGroups().elementAt(g); + + if(sg.cs == null) + continue; - if (cs instanceof ResidueColourScheme) + + /* if (view.getAnnotationColours().getColourScheme().equals("None")) + { + sg.cs = new AnnotationColourGradient( + af.viewport.alignment.getAlignmentAnnotation()[i], + new java.awt.Color(view.getAnnotationColours(). + getMinColour()), + new java.awt.Color(view.getAnnotationColours(). + getMaxColour()), + view.getAnnotationColours().getAboveThreshold()); + } + else*/ + { + sg.cs = new AnnotationColourGradient( + af.viewport.alignment.getAlignmentAnnotation()[i], + sg.cs, + view.getAnnotationColours().getAboveThreshold() + ); + } + + } + + + break; + } + + } + } + else { - ((ResidueColourScheme) cs).setThreshold(view.getPidThreshold(), true); + cs = ColourSchemeProperty.getColour(al, view.getBgColour()); } if(cs!=null) + { + cs.setThreshold(view.getPidThreshold(), true); cs.setConsensus(af.viewport.vconsensus); + } } af.setColourSelected(view.getBgColour()); af.viewport.setGlobalColourScheme(cs); af.viewport.setColourAppliesToAllGroups(false); - af.changeColour(af.viewport.getGlobalColourScheme()); - if (view.getConservationSelected()) + af.changeColour(cs); + if (view.getConservationSelected() && cs!=null) { - ( (ConservationColourScheme) af.viewport.getGlobalColourScheme()).inc = view.getConsThreshold(); + cs.setConservationInc(view.getConsThreshold()); } af.viewport.setColourAppliesToAllGroups(true); if (view.getShowSequenceFeatures()) { - af.viewport.showSequenceFeatures = true; - af.sequenceFeatures.setSelected(true); - new SequenceFeatureFetcher(al, af.alignPanel); - al.featuresAdded = true; + af.viewport.showSequenceFeatures = true; + af.showSeqFeatures.setSelected(true); } + if(jms.getFeatureSettings()!=null) + { + af.viewport.featuresDisplayed = new Hashtable(); + String [] renderOrder = new String[jms.getFeatureSettings().getSettingCount()]; + for(int fs=0; fs 0) @@ -770,35 +1092,45 @@ public class Jalview2XML { for (int t = 0; t < jms.getTreeCount(); t++) { + Tree tree = jms.getTree(t); TreePanel tp = af.ShowNewickTree(new jalview.io.NewickFile( - tree.getNewick()), tree.getTitle()); - - tp.setBounds(tree.getXpos(), tree.getYpos(), - tree.getWidth(), tree.getHeight()); + tree.getNewick()), tree.getTitle(), + tree.getWidth(), tree.getHeight(), + tree.getXpos(), tree.getYpos()); tp.fitToWindow.setState(tree.getFitToWindow()); tp.fitToWindow_actionPerformed(null); - tp.treeCanvas.fontSize = tree.getFontSize(); - tp.fontSize.setText("Font Size - " + tree.getFontSize()); - tp.placeholdersMenu.setState(tree.getMarkUnlinked()); - tp.placeholdersMenu_actionPerformed(null); - tp.bootstrapMenu.setState(tree.getShowBootstrap()); - tp.bootstrapMenu_actionPerformed(null); - tp.distanceMenu.setState(tree.getShowDistances()); - tp.distanceMenu_actionPerformed(null); + + if(tree.getFontName()!=null) + tp.setTreeFont(new java.awt.Font(tree.getFontName(), + tree.getFontStyle(), + tree.getFontSize())); + else + tp.setTreeFont(new java.awt.Font(view.getFontName(), + view.getFontStyle(), + tree.getFontSize())); + + tp.showPlaceholders(tree.getMarkUnlinked()); + tp.showBootstrap(tree.getShowBootstrap()); + tp.showDistances(tree.getShowDistances()); + tp.treeCanvas.threshold = tree.getThreshold(); if (tree.getCurrentTree()) af.viewport.setCurrentTree(tp.getTree()); } + } catch (Exception ex) { ex.printStackTrace(); } + } + return af; } } +