X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FJalview2XML.java;h=a3604d67c0b93dcc3ee618dde69e563f4584ceb2;hb=c7633fc4fc9799d9a906c8b60b3e3981a2c0b4fb;hp=23b09deb1ba8a7f61622c450f56091ea0b81e0b3;hpb=06e3a52df5af8243cdb67c023c8ddd834711ad36;p=jalview.git diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java index 23b09de..a3604d6 100644 --- a/src/jalview/gui/Jalview2XML.java +++ b/src/jalview/gui/Jalview2XML.java @@ -20,6 +20,7 @@ */ package jalview.gui; +import jalview.api.ViewStyleI; import jalview.api.structures.JalviewStructureDisplayI; import jalview.bin.Cache; import jalview.datamodel.AlignedCodonFrame; @@ -78,6 +79,7 @@ import jalview.structure.StructureSelectionManager; import jalview.structures.models.AAStructureBindingModel; import jalview.util.MessageManager; import jalview.util.Platform; +import jalview.util.StringUtils; import jalview.util.jarInputStreamProvider; import jalview.viewmodel.AlignmentViewport; import jalview.viewmodel.seqfeatures.FeatureRendererSettings; @@ -89,6 +91,7 @@ import jalview.ws.params.ArgumentI; import jalview.ws.params.AutoCalcSetting; import jalview.ws.params.WsParamSetI; +import java.awt.Color; import java.awt.Rectangle; import java.io.BufferedReader; import java.io.DataInputStream; @@ -115,7 +118,6 @@ import java.util.List; import java.util.Map; import java.util.Map.Entry; import java.util.Set; -import java.util.StringTokenizer; import java.util.Vector; import java.util.jar.JarEntry; import java.util.jar.JarInputStream; @@ -162,7 +164,7 @@ public class Jalview2XML */ Map seqRefIds = null; - Vector frefedSequence = null; + Vector frefedSequence = null; boolean raiseGUI = true; // whether errors are raised in dialog boxes or not @@ -257,7 +259,7 @@ public class Jalview2XML int r = 0, rSize = frefedSequence.size(); while (r < rSize) { - Object[] ref = (Object[]) frefedSequence.elementAt(r); + Object[] ref = frefedSequence.elementAt(r); if (ref != null) { String sref = (String) ref[0]; @@ -760,10 +762,11 @@ public class Jalview2XML if (sf[index].otherDetails != null) { String key; - Enumeration keys = sf[index].otherDetails.keys(); - while (keys.hasMoreElements()) + Iterator keys = sf[index].otherDetails.keySet() + .iterator(); + while (keys.hasNext()) { - key = keys.nextElement().toString(); + key = keys.next(); OtherData keyValue = new OtherData(); keyValue.setKey(key); keyValue.setValue(sf[index].otherDetails.get(key).toString()); @@ -878,7 +881,7 @@ public class Jalview2XML // SAVE MAPPINGS if (jal.getCodonFrames() != null) { - Set jac = jal.getCodonFrames(); + List jac = jal.getCodonFrames(); for (AlignedCodonFrame acf : jac) { AlcodonFrame alc = new AlcodonFrame(); @@ -1091,15 +1094,26 @@ public class Jalview2XML view.setViewName(av.viewName); view.setGatheredViews(av.isGatherViewsHere()); - Rectangle position = ap.av.getExplodedGeometry(); - if (position == null) + Rectangle size = ap.av.getExplodedGeometry(); + Rectangle position = size; + if (size == null) { - position = ap.alignFrame.getBounds(); + size = ap.alignFrame.getBounds(); + if (av.getCodingComplement() != null) + { + position = ((SplitFrame) ap.alignFrame.getSplitViewContainer()) + .getBounds(); + } + else + { + position = size; + } } view.setXpos(position.x); view.setYpos(position.y); - view.setWidth(position.width); - view.setHeight(position.height); + + view.setWidth(size.width); + view.setHeight(size.height); view.setStartRes(av.startRes); view.setStartSeq(av.startSeq); @@ -1149,6 +1163,7 @@ public class Jalview2XML view.setFontName(av.font.getName()); view.setFontSize(av.font.getSize()); view.setFontStyle(av.font.getStyle()); + view.setScaleProteinAsCdna(av.getViewStyle().isScaleProteinAsCdna()); view.setRenderGaps(av.isRenderGaps()); view.setShowAnnotation(av.isShowAnnotation()); view.setShowBoxes(av.getShowBoxes()); @@ -1180,17 +1195,17 @@ public class Jalview2XML .getFeatureRenderer().getRenderOrder() .toArray(new String[0]); - Vector settingsAdded = new Vector(); + Vector settingsAdded = new Vector(); Object gstyle = null; GraduatedColor gcol = null; if (renderOrder != null) { - for (int ro = 0; ro < renderOrder.length; ro++) + for (String featureType : renderOrder) { gstyle = ap.getSeqPanel().seqCanvas.getFeatureRenderer() - .getFeatureStyle(renderOrder[ro]); + .getFeatureStyle(featureType); Setting setting = new Setting(); - setting.setType(renderOrder[ro]); + setting.setType(featureType); if (gstyle instanceof GraduatedColor) { gcol = (GraduatedColor) gstyle; @@ -1205,57 +1220,30 @@ public class Jalview2XML } else { - setting.setColour(ap.getSeqPanel().seqCanvas - .getFeatureRenderer().getColour(renderOrder[ro]) - .getRGB()); + setting.setColour(((Color) gstyle).getRGB()); } setting.setDisplay(av.getFeaturesDisplayed().isVisible( - renderOrder[ro])); + featureType)); float rorder = ap.getSeqPanel().seqCanvas.getFeatureRenderer() - .getOrder(renderOrder[ro]); + .getOrder(featureType); if (rorder > -1) { setting.setOrder(rorder); } fs.addSetting(setting); - settingsAdded.addElement(renderOrder[ro]); + settingsAdded.addElement(featureType); } } - // Make sure we save none displayed feature settings - Iterator en = ap.getSeqPanel().seqCanvas.getFeatureRenderer() - .getFeatureColours().keySet().iterator(); - while (en.hasNext()) - { - String key = en.next().toString(); - if (settingsAdded.contains(key)) - { - continue; - } - - Setting setting = new Setting(); - setting.setType(key); - setting.setColour(ap.getSeqPanel().seqCanvas.getFeatureRenderer() - .getColour(key).getRGB()); - - setting.setDisplay(false); - float rorder = ap.getSeqPanel().seqCanvas.getFeatureRenderer() - .getOrder(key); - if (rorder > -1) - { - setting.setOrder(rorder); - } - fs.addSetting(setting); - settingsAdded.addElement(key); - } // is groups actually supposed to be a map here ? - en = ap.getSeqPanel().seqCanvas.getFeatureRenderer() + Iterator en = ap.getSeqPanel().seqCanvas + .getFeatureRenderer() .getFeatureGroups().iterator(); - Vector groupsAdded = new Vector(); + Vector groupsAdded = new Vector(); while (en.hasNext()) { - String grp = en.next().toString(); + String grp = en.next(); if (groupsAdded.contains(grp)) { continue; @@ -1852,8 +1840,8 @@ public class Jalview2XML } } throw new Error(MessageManager.formatMessage( - "error.unsupported_version_calcIdparam", new Object[] - { calcIdParam.toString() })); + "error.unsupported_version_calcIdparam", + new Object[] { calcIdParam.toString() })); } /** @@ -1935,16 +1923,16 @@ public class Jalview2XML if (jds.getDatasetSequence() != null) { vamsasSeq.setDsseqid(seqHash(jds.getDatasetSequence())); - if (jds.getDatasetSequence().getDBRef() != null) + if (jds.getDatasetSequence().getDBRefs() != null) { - dbrefs = jds.getDatasetSequence().getDBRef(); + dbrefs = jds.getDatasetSequence().getDBRefs(); } } else { vamsasSeq.setDsseqid(id); // so we can tell which sequences really are // dataset sequences only - dbrefs = jds.getDBRef(); + dbrefs = jds.getDBRefs(); } if (dbrefs != null) { @@ -2165,6 +2153,7 @@ public class Jalview2XML { SwingUtilities.invokeAndWait(new Runnable() { + @Override public void run() { setLoadingFinishedForNewStructureViewers(); @@ -2239,7 +2228,7 @@ public class Jalview2XML } if (frefedSequence == null) { - frefedSequence = new Vector(); + frefedSequence = new Vector(); } AlignFrame af = null, _af = null; @@ -2451,6 +2440,11 @@ public class Jalview2XML int width = (int) dnaFrame.getBounds().getWidth(); int height = (int) (dnaFrame.getBounds().getHeight() + proteinFrame.getBounds().getHeight() + 50); + + /* + * SplitFrame location is saved to both enclosed frames + */ + splitFrame.setLocation(dnaFrame.getX(), dnaFrame.getY()); Desktop.addInternalFrame(splitFrame, title, width, height); /* @@ -2830,15 +2824,15 @@ public class Jalview2XML { mapping = addMapping(maps[m].getMapping()); } - if (dnaseq != null) + if (dnaseq != null && mapping.getTo() != null) { cf.addMap(dnaseq, mapping.getTo(), mapping.getMap()); } else { // defer to later - frefedSequence.add(new Object[] - { maps[m].getDnasq(), cf, mapping }); + frefedSequence.add(new Object[] { maps[m].getDnasq(), cf, + mapping }); } } } @@ -3248,8 +3242,8 @@ public class Jalview2XML * indicate that annotation colours are applied across all groups (pre * Jalview 2.8.1 behaviour) */ - boolean doGroupAnnColour = isVersionStringLaterThan("2.8.1", - object.getVersion()); + boolean doGroupAnnColour = Jalview2XML.isVersionStringLaterThan( + "2.8.1", object.getVersion()); AlignmentPanel ap = null; boolean isnewview = true; @@ -4027,18 +4021,22 @@ public class Jalview2XML } /** + * Answers true if 'version' is equal to or later than 'supported', where each + * is formatted as major/minor versions like "2.8.3" or "2.3.4b1" for bugfix + * changes. Development and test values for 'version' are leniently treated + * i.e. answer true. * * @param supported * - minimum version we are comparing against * @param version - * - version of data being processsed. - * @return true if version is development/null or evaluates to the same or - * later X.Y.Z (where X,Y,Z are like [0-9]+b?[0-9]*) + * - version of data being processsed + * @return */ - protected boolean isVersionStringLaterThan(String supported, + public static boolean isVersionStringLaterThan(String supported, String version) { - if (version == null || version.equalsIgnoreCase("DEVELOPMENT BUILD") + if (supported == null || version == null + || version.equalsIgnoreCase("DEVELOPMENT BUILD") || version.equalsIgnoreCase("Test") || version.equalsIgnoreCase("AUTOMATED BUILD")) { @@ -4049,38 +4047,8 @@ public class Jalview2XML } else { - StringTokenizer currentV = new StringTokenizer(supported, "."), fileV = new StringTokenizer( - version, "."); - while (currentV.hasMoreTokens() && fileV.hasMoreTokens()) - { - // convert b to decimal to catch bugfix releases within a series - String curT = currentV.nextToken().toLowerCase().replace('b', '.'); - String fileT = fileV.nextToken().toLowerCase().replace('b', '.'); - try - { - if (Float.valueOf(curT) > Float.valueOf(fileT)) - { - // current version is newer than the version that wrote the file - return false; - } - } catch (NumberFormatException nfe) - { - System.err - .println("** WARNING: Version comparison failed for tokens (" - + curT - + ") and (" - + fileT - + ")\n** Current: '" - + supported + "' and Version: '" + version + "'"); - } - } - if (currentV.hasMoreElements()) - { - // fileV has no minor version but identical series to current - return false; - } + return StringUtils.compareVersions(version, supported, "b") >= 0; } - return true; } Vector newStructureViewers = null; @@ -4194,6 +4162,9 @@ public class Jalview2XML af.viewport.setFont( new java.awt.Font(view.getFontName(), view.getFontStyle(), view .getFontSize()), true); + ViewStyleI vs = af.viewport.getViewStyle(); + vs.setScaleProteinAsCdna(view.isScaleProteinAsCdna()); + af.viewport.setViewStyle(vs); // TODO: allow custom charWidth/Heights to be restored by updating them // after setting font - which means set above to false af.viewport.setRenderGaps(view.getRenderGaps()); @@ -4578,8 +4549,8 @@ public class Jalview2XML /** * Kludge for magic autoannotation names (see JAL-811) */ - String[] magicNames = new String[] - { "Consensus", "Quality", "Conservation" }; + String[] magicNames = new String[] { "Consensus", "Quality", + "Conservation" }; JvAnnotRow nullAnnot = new JvAnnotRow(-1, null); Hashtable visan = new Hashtable(); for (String nm : magicNames) @@ -4989,8 +4960,7 @@ public class Jalview2XML } else { - frefedSequence.add(new Object[] - { dsfor, jmap }); + frefedSequence.add(new Object[] { dsfor, jmap }); } } else