X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FJalview2XML.java;h=b608b9502fcd41dc8e4b57c94a7eebb264f8dbfe;hb=5019d046ada4f11d4273f8e826961a90b4405947;hp=90fef074e967efe9ebac71f545ac97df4f0ceef4;hpb=003f3b92bdb5672e3ce961fcad6e69bc45f916b9;p=jalview.git diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java index 90fef07..b608b95 100644 --- a/src/jalview/gui/Jalview2XML.java +++ b/src/jalview/gui/Jalview2XML.java @@ -1,42 +1,71 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1) + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2) * Copyright (C) 2014 The Jalview Authors * * This file is part of Jalview. * * Jalview is free software: you can redistribute it and/or * modify it under the terms of the GNU General Public License - * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. + * as published by the Free Software Foundation, either version 3 + * of the License, or (at your option) any later version. * * Jalview is distributed in the hope that it will be useful, but * WITHOUT ANY WARRANTY; without even the implied warranty * of MERCHANTABILITY or FITNESS FOR A PARTICULAR * PURPOSE. See the GNU General Public License for more details. * - * You should have received a copy of the GNU General Public License along with Jalview. If not, see . + * You should have received a copy of the GNU General Public License + * along with Jalview. If not, see . * The Jalview Authors are detailed in the 'AUTHORS' file. */ package jalview.gui; -import java.awt.Rectangle; -import java.io.*; -import java.lang.reflect.InvocationTargetException; -import java.net.*; -import java.util.*; -import java.util.Map.Entry; -import java.util.jar.*; - -import javax.swing.*; - -import org.exolab.castor.xml.*; - +import jalview.api.structures.JalviewStructureDisplayI; import jalview.bin.Cache; import jalview.datamodel.Alignment; import jalview.datamodel.AlignmentAnnotation; import jalview.datamodel.AlignmentI; import jalview.datamodel.SequenceI; -import jalview.schemabinding.version2.*; -import jalview.schemes.*; +import jalview.schemabinding.version2.AlcodMap; +import jalview.schemabinding.version2.Alcodon; +import jalview.schemabinding.version2.AlcodonFrame; +import jalview.schemabinding.version2.Annotation; +import jalview.schemabinding.version2.AnnotationColours; +import jalview.schemabinding.version2.AnnotationElement; +import jalview.schemabinding.version2.CalcIdParam; +import jalview.schemabinding.version2.DBRef; +import jalview.schemabinding.version2.Features; +import jalview.schemabinding.version2.Group; +import jalview.schemabinding.version2.HiddenColumns; +import jalview.schemabinding.version2.JGroup; +import jalview.schemabinding.version2.JSeq; +import jalview.schemabinding.version2.JalviewModel; +import jalview.schemabinding.version2.JalviewModelSequence; +import jalview.schemabinding.version2.MapListFrom; +import jalview.schemabinding.version2.MapListTo; +import jalview.schemabinding.version2.Mapping; +import jalview.schemabinding.version2.MappingChoice; +import jalview.schemabinding.version2.OtherData; +import jalview.schemabinding.version2.PdbentryItem; +import jalview.schemabinding.version2.Pdbids; +import jalview.schemabinding.version2.Property; +import jalview.schemabinding.version2.Sequence; +import jalview.schemabinding.version2.SequenceSet; +import jalview.schemabinding.version2.SequenceSetProperties; +import jalview.schemabinding.version2.Setting; +import jalview.schemabinding.version2.StructureState; +import jalview.schemabinding.version2.ThresholdLine; +import jalview.schemabinding.version2.Tree; +import jalview.schemabinding.version2.UserColours; +import jalview.schemabinding.version2.Viewport; +import jalview.schemes.AnnotationColourGradient; +import jalview.schemes.ColourSchemeI; +import jalview.schemes.ColourSchemeProperty; +import jalview.schemes.GraduatedColor; +import jalview.schemes.ResidueColourScheme; +import jalview.schemes.ResidueProperties; +import jalview.structure.StructureSelectionManager; +import jalview.util.MessageManager; import jalview.util.Platform; import jalview.util.jarInputStreamProvider; import jalview.viewmodel.AlignmentViewport; @@ -47,6 +76,41 @@ import jalview.ws.params.ArgumentI; import jalview.ws.params.AutoCalcSetting; import jalview.ws.params.WsParamSetI; +import java.awt.Rectangle; +import java.io.BufferedReader; +import java.io.DataInputStream; +import java.io.DataOutputStream; +import java.io.File; +import java.io.FileInputStream; +import java.io.FileOutputStream; +import java.io.IOException; +import java.io.InputStreamReader; +import java.io.OutputStreamWriter; +import java.io.PrintWriter; +import java.lang.reflect.InvocationTargetException; +import java.net.MalformedURLException; +import java.net.URL; +import java.util.ArrayList; +import java.util.Enumeration; +import java.util.HashSet; +import java.util.Hashtable; +import java.util.IdentityHashMap; +import java.util.Iterator; +import java.util.List; +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; +import java.util.jar.JarOutputStream; + +import javax.swing.JInternalFrame; +import javax.swing.JOptionPane; +import javax.swing.SwingUtilities; + +import org.exolab.castor.xml.Unmarshaller; + /** * Write out the current jalview desktop state as a Jalview XML stream. * @@ -434,7 +498,7 @@ public class Jalview2XML for (String dssids : dsses.keySet()) { AlignFrame _af = dsses.get(dssids); - String jfileName = fileName + " Dataset for " + _af.getTitle(); + String jfileName = MessageManager.formatMessage("label.dataset_for", new String[]{fileName,_af.getTitle()}); if (!jfileName.endsWith(".xml")) { jfileName = jfileName + ".xml"; @@ -674,7 +738,9 @@ public class Jalview2XML .startsWith( jmol.jmb.pdbentry[peid].getId() .toLowerCase()))) + { continue; + } if (matchedFile == null) { matchedFile = jmol.jmb.pdbentry[peid].getFile(); @@ -1353,7 +1419,16 @@ public class Jalview2XML calcIdSet.add(aa[i].getCalcId()); an.setCalcId(aa[i].getCalcId()); } - + if (aa[i].hasProperties()) + { + for (String pr : aa[i].getProperties()) + { + Property prop = new Property(); + prop.setName(pr); + prop.setValue(aa[i].getProperty(pr)); + an.addProperty(prop); + } + } AnnotationElement ae; if (aa[i].annotations != null) { @@ -1367,18 +1442,26 @@ public class Jalview2XML ae = new AnnotationElement(); if (aa[i].annotations[a].description != null) + { ae.setDescription(aa[i].annotations[a].description); + } if (aa[i].annotations[a].displayCharacter != null) + { ae.setDisplayCharacter(aa[i].annotations[a].displayCharacter); + } if (!Float.isNaN(aa[i].annotations[a].value)) + { ae.setValue(aa[i].annotations[a].value); + } ae.setPosition(a); if (aa[i].annotations[a].secondaryStructure != ' ' && aa[i].annotations[a].secondaryStructure != '\0') + { ae.setSecondaryStructure(aa[i].annotations[a].secondaryStructure + ""); + } if (aa[i].annotations[a].colour != null && aa[i].annotations[a].colour != java.awt.Color.black) @@ -1499,8 +1582,7 @@ public class Jalview2XML return false; } } - throw new Error("Unsupported Version for calcIdparam " - + calcIdParam.toString()); + throw new Error(MessageManager.formatMessage("error.unsupported_version_calcIdparam", new String[]{calcIdParam.toString()})); } /** @@ -1793,7 +1875,7 @@ public class Jalview2XML try { // create list to store references for any new Jmol viewers created - newStructureViewers = new Vector(); + newStructureViewers = new Vector(); // UNMARSHALLER SEEMS TO CLOSE JARINPUTSTREAM, MOST ANNOYING // Workaround is to make sure caller implements the JarInputStreamProvider // interface @@ -2043,7 +2125,7 @@ public class Jalview2XML errorMessage = null; } - Hashtable alreadyLoadedPDB; + Hashtable alreadyLoadedPDB; /** * when set, local views will be updated from view stored in JalviewXML @@ -2055,10 +2137,14 @@ public class Jalview2XML String loadPDBFile(jarInputStreamProvider jprovider, String pdbId) { if (alreadyLoadedPDB == null) + { alreadyLoadedPDB = new Hashtable(); + } if (alreadyLoadedPDB.containsKey(pdbId)) + { return alreadyLoadedPDB.get(pdbId).toString(); + } try { @@ -2290,7 +2376,9 @@ public class Jalview2XML entry.setFile(pdbloaded.get(ids[p].getId()).toString()); } } - + StructureSelectionManager.getStructureSelectionManager( + Desktop.instance) + .registerPDBEntry(entry); al.getSequenceAt(i).getDatasetSequence().addPDBId(entry); } } @@ -2406,7 +2494,9 @@ public class Jalview2XML // in principle Visible should always be true for annotation displayed // in multiple views if (an[i].hasVisible()) + { jda.visible = an[i].getVisible(); + } al.addAnnotation(jda); @@ -2425,7 +2515,9 @@ public class Jalview2XML anpos = ae[aa].getPosition(); if (anpos >= anot.length) + { continue; + } anot[anpos] = new jalview.datamodel.Annotation( @@ -2519,10 +2611,14 @@ public class Jalview2XML jaa.setScore(an[i].getScore()); } if (an[i].hasVisible()) + { jaa.visible = an[i].getVisible(); + } if (an[i].hasCentreColLabels()) + { jaa.centreColLabels = an[i].getCentreColLabels(); + } if (an[i].hasScaleColLabels()) { @@ -2544,7 +2640,14 @@ public class Jalview2XML jaa.belowAlignment = an[i].isBelowAlignment(); } jaa.setCalcId(an[i].getCalcId()); - + if (an[i].getPropertyCount() > 0) + { + for (jalview.schemabinding.version2.Property prop : an[i] + .getProperty()) + { + jaa.setProperty(prop.getName(), prop.getValue()); + } + } if (jaa.autoCalculated) { autoAlan.add(new JvAnnotRow(i, jaa)); @@ -3130,10 +3233,11 @@ public class Jalview2XML @Override public void run() { - AppJmol sview = null; + JalviewStructureDisplayI sview = null; try { - sview = new AppJmol(pdbf, id, sq, alf.alignPanel, + // JAL-1333 note - we probably can't migrate Jmol views to UCSF Chimera! + sview = new StructureViewer(alf.alignPanel.getStructureSelectionManager()).createView(StructureViewer.Viewer.JMOL, pdbf, id, sq, alf.alignPanel, useinJmolsuperpos, usetoColourbyseq, jmolColouring, fileloc, rect, vid); addNewStructureViewer(sview); @@ -3209,15 +3313,18 @@ public class Jalview2XML /** * - * @param supported - minimum version we are comparing against - * @param version - version of data being processsed. + * @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]*) */ private boolean isVersionStringLaterThan(String supported, String version) { if (version == null || version.equalsIgnoreCase("DEVELOPMENT BUILD") - || version.equalsIgnoreCase("Test")) + || version.equalsIgnoreCase("Test") + || version.equalsIgnoreCase("AUTOMATED BUILD")) { System.err.println("Assuming project file with " + (version == null ? "null" : version) @@ -3260,13 +3367,13 @@ public class Jalview2XML return true; } - Vector newStructureViewers = null; + Vector newStructureViewers = null; - protected void addNewStructureViewer(AppJmol sview) + protected void addNewStructureViewer(JalviewStructureDisplayI sview) { if (newStructureViewers != null) { - sview.jmb.setFinishedLoadingFromArchive(false); + sview.getBinding().setFinishedLoadingFromArchive(false); newStructureViewers.add(sview); } } @@ -3275,9 +3382,9 @@ public class Jalview2XML { if (newStructureViewers != null) { - for (AppJmol sview : newStructureViewers) + for (JalviewStructureDisplayI sview : newStructureViewers) { - sview.jmb.setFinishedLoadingFromArchive(true); + sview.getBinding().setFinishedLoadingFromArchive(true); } newStructureViewers.clear(); newStructureViewers = null; @@ -3537,12 +3644,16 @@ public class Jalview2XML } renderOrder[fs] = setting.getType(); if (setting.hasOrder()) + { af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setOrder( setting.getType(), setting.getOrder()); + } else + { af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setOrder( setting.getType(), fs / jms.getFeatureSettings().getSettingCount()); + } if (setting.getDisplay()) { af.viewport.featuresDisplayed.put(setting.getType(), new Integer( @@ -4385,7 +4496,9 @@ public class Jalview2XML } } else + { Cache.log.debug("Ignoring " + jvobj.getClass() + " (ID = " + id); + } } }