From 2be3bda24ceee2da9d3c41723b5bc1e660948a20 Mon Sep 17 00:00:00 2001 From: amwaterhouse Date: Tue, 4 Apr 2006 09:30:27 +0000 Subject: [PATCH] Uses descriptors --- src/jalview/gui/Jalview2XML_V1.java | 488 +++++++++++++++++++++++++++++++++++ 1 file changed, 488 insertions(+) create mode 100755 src/jalview/gui/Jalview2XML_V1.java diff --git a/src/jalview/gui/Jalview2XML_V1.java b/src/jalview/gui/Jalview2XML_V1.java new file mode 100755 index 0000000..d84b8db --- /dev/null +++ b/src/jalview/gui/Jalview2XML_V1.java @@ -0,0 +1,488 @@ +/* + * Jalview - A Sequence Alignment Editor and Viewer + * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * + * This program 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 2 + * of the License, or (at your option) any later version. + * + * This program 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 this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA + */ +package jalview.gui; + +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.binding.*; + + + + +/** + * DOCUMENT ME! + * + * @author $author$ + * @version $Revision$ + */ +public class Jalview2XML_V1 +{ + jalview.schemes.UserColourScheme GetUserColourScheme( + JalviewModelSequence jms, String id) + { + UserColours[] uc = jms.getUserColours(); + UserColours colours = null; + + for (int i = 0; i < uc.length; i++) + { + if (uc[i].getId().equals(id)) + { + colours = uc[i]; + + break; + } + } + + int csize = colours.getUserColourScheme().getColourCount(); + java.awt.Color[] newColours = new java.awt.Color[csize]; + + for (int i = 0; i < csize; i++) + { + newColours[i] = new java.awt.Color(Integer.parseInt( + colours.getUserColourScheme().getColour(i).getRGB(), 16)); + } + + return new jalview.schemes.UserColourScheme(newColours); + } + + /** + * DOCUMENT ME! + * + * @param file DOCUMENT ME! + */ + public AlignFrame LoadJalviewAlign(String file) + { + + jalview.gui.AlignFrame af = null; + + try + { + //UNMARSHALLER SEEMS TO CLOSE JARINPUTSTREAM, MOST ANNOYING + URL url = null; + + if (file.startsWith("http://")) + { + url = new URL(file); + } + + JarInputStream jin = null; + JarEntry jarentry = null; + int entryCount = 1; + + do + { + if (url != null) + { + jin = new JarInputStream(url.openStream()); + } + else + { + jin = new JarInputStream(new FileInputStream(file)); + } + + for (int i = 0; i < entryCount; i++) + { + jarentry = jin.getNextJarEntry(); + + } + + + class NoDescIDResolver implements IDResolver + { + public Object resolve(String idref) + { + System.out.println(idref+" used"); + return null; + } + } + + + if (jarentry != null) + { + InputStreamReader in = new InputStreamReader(jin, "UTF-8"); + JalviewModel object = new JalviewModel(); + + object = (JalviewModel) object.unmarshal(in); + + af = LoadFromObject(object); + entryCount++; + } + } + while (jarentry != null); + } + catch(java.net.UnknownHostException ex) + { + ex.printStackTrace(); + System.err.println("Couldn't locate Jalview XML file : " + + ex + "\n"); + JOptionPane.showInternalMessageDialog(Desktop.desktop, + "Couldn't locate " + file, + "URL not found", + JOptionPane.WARNING_MESSAGE); + + } + catch (Exception ex) + { + ex.printStackTrace(); + System.err.println("Exception whilst loading jalview XML file : " + + ex + "\n"); + JOptionPane.showInternalMessageDialog(Desktop.desktop, + "Error loading " + file, + "Error loading Jalview file", + JOptionPane.WARNING_MESSAGE); + + } + + return af; + } + + AlignFrame LoadFromObject(JalviewModel object) + { + Vector seqids = new Vector(); + SequenceSet vamsasSet = object.getVamsasModel().getSequenceSet(0); + Sequence[] vamsasSeq = vamsasSet.getSequence(); + + JalviewModelSequence jms = object.getJalviewModelSequence(); + + ////////////////////////////////// + //LOAD SEQUENCES + jalview.datamodel.Sequence[] jseqs = new jalview.datamodel.Sequence[vamsasSeq.length]; + JSeq[] JSEQ = object.getJalviewModelSequence().getJSeq(); + for (int i = 0; i < vamsasSeq.length; i++) + { + jseqs[i] = new jalview.datamodel.Sequence(vamsasSeq[i].getName(), + vamsasSeq[i].getSequence()); + jseqs[i].setStart(JSEQ[i].getStart()); + jseqs[i].setEnd(JSEQ[i].getEnd()); + jseqs[i].setColor(new java.awt.Color(JSEQ[i].getColour())); + seqids.add(jseqs[i]); + } + + ///SequenceFeatures are added to the DatasetSequence, + // so we must create the dataset before loading features + ///////////////////////////////// + jalview.datamodel.Alignment al = new jalview.datamodel.Alignment(jseqs); + al.setDataset(null); + ///////////////////////////////// + + for (int i = 0; i < vamsasSeq.length; i++) + { + if (JSEQ[i].getFeaturesCount() > 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(), + null); + + 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) + { + Annotation[] an = vamsasSet.getAnnotation(); + + for (int i = 0; i < an.length; i++) + { + AnnotationElement[] ae = an[i].getAnnotationElement(); + jalview.datamodel.Annotation[] anot = new jalview.datamodel.Annotation[al.getWidth()]; + + for (int aa = 0; aa < ae.length; aa++) + { + anot[ae[aa].getPosition()] = new jalview.datamodel.Annotation(ae[aa].getDisplayCharacter(), + ae[aa].getDescription(), + ae[aa].getSecondaryStructure().charAt(0), + ae[aa].getValue()); + } + + jalview.datamodel.AlignmentAnnotation jaa = null; + + if (an[i].getGraph()) + { + jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(), + an[i].getDescription(), anot, 0, 0, + jalview.datamodel.AlignmentAnnotation.BAR_GRAPH); + } + else + { + jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(), + an[i].getDescription(), anot); + } + + al.addAnnotation(jaa); + } + } + + + ///////////////////////////////// + // LOAD VIEWPORT + Viewport[] views = jms.getViewport(); + Viewport view = views[0]; // DEAL WITH MULTIPLE VIEWPORTS LATER + + AlignFrame af = new AlignFrame(al); + + + // af.changeColour() ); + ///////////////////////// + //LOAD GROUPS + if (jms.getJGroupCount() > 0) + { + JGroup[] groups = jms.getJGroup(); + + for (int i = 0; i < groups.length; i++) + { + ColourSchemeI cs = null; + + if (groups[i].getColour() != null) + { + if (groups[i].getColour().startsWith("ucs")) + { + cs = GetUserColourScheme(jms, groups[i].getColour()); + } + else + { + cs = ColourSchemeProperty.getColour(al, + groups[i].getColour()); + } + + cs.setThreshold(groups[i].getPidThreshold(), true); + } + + Vector seqs = new Vector(); + int[] ids = groups[i].getSeq(); + + for (int s = 0; s < ids.length; s++) + { + seqs.addElement((jalview.datamodel.SequenceI) seqids.elementAt( + ids[s])); + } + + jalview.datamodel.SequenceGroup sg = new jalview.datamodel.SequenceGroup(seqs, + groups[i].getName(), cs, groups[i].getDisplayBoxes(), + groups[i].getDisplayText(), groups[i].getColourText(), + groups[i].getStart(), groups[i].getEnd()); + + sg.setOutlineColour(new java.awt.Color( + groups[i].getOutlineColour())); + + if (groups[i].getConsThreshold() != 0) + { + jalview.analysis.Conservation c = new jalview.analysis.Conservation("All", + ResidueProperties.propHash, 3, sg.sequences, 0, + sg.getWidth() - 1); + c.calculate(); + c.verdict(false, 25); + sg.cs.setConservation(c); + } + + al.addGroup(sg); + } + } + + + + 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(); + af.viewport.setAbovePIDThreshold(view.getPidSelected()); + af.abovePIDThreshold.setSelected(view.getPidSelected()); + af.viewport.setColourText(view.getShowColourText()); + af.colourTextMenuItem.setSelected(view.getShowColourText()); + af.viewport.setConservationSelected(view.getConservationSelected()); + af.conservationMenuItem.setSelected(view.getConservationSelected()); + + af.viewport.setShowJVSuffix(view.getShowFullId()); + af.seqLimits.setSelected(view.getShowFullId()); + + af.viewport.setFont(new java.awt.Font(view.getFontName(), + view.getFontStyle(), view.getFontSize())); + af.alignPanel.fontChanged(); + + af.viewport.setRenderGaps(view.getRenderGaps()); + af.renderGapsMenuItem.setSelected(view.getRenderGaps()); + + af.viewport.setWrapAlignment(view.getWrapAlignment()); + af.wrapMenuItem.setSelected(view.getWrapAlignment()); + + if (view.getWrapAlignment()) + { + af.alignPanel.setWrapAlignment(view.getWrapAlignment()); + } + else + { + af.annotationPanelMenuItem.setState(view.getShowAnnotation()); + af.viewport.setShowAnnotation(view.getShowAnnotation()); + af.alignPanel.setAnnotationVisible(view.getShowAnnotation()); + } + + af.viewport.setShowBoxes(view.getShowBoxes()); + af.viewBoxesMenuItem.setSelected(view.getShowBoxes()); + af.viewport.setShowText(view.getShowText()); + af.viewTextMenuItem.setSelected(view.getShowText()); + + ColourSchemeI cs = null; + + if (view.getBgColour() != null) + { + if (view.getBgColour().startsWith("ucs")) + { + cs = GetUserColourScheme(jms, view.getBgColour()); + } + else + { + 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(cs); + if (view.getConservationSelected() && cs!=null) + { + cs.setConservationInc(view.getConsThreshold()); + } + + af.viewport.setColourAppliesToAllGroups(true); + + if (view.getShowSequenceFeatures()) + { + 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) + { + try + { + 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(), + tree.getWidth(), tree.getHeight(), + tree.getXpos(), tree.getYpos()); + + tp.fitToWindow.setState(tree.getFitToWindow()); + tp.fitToWindow_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; + } +} + -- 1.7.10.2