X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FJalview2XML_V1.java;h=cc2f63603ca65e00662471670e64ae927ec626ed;hb=e67e5f3a5b922e8a7729a0e9e9b174f46b11456c;hp=586e2faf1e9b9b1ebf6fdb79dfa2cb8eb651cd02;hpb=30133ea9afab31009432eb013c299eb6c36ae75e;p=jalview.git diff --git a/src/jalview/gui/Jalview2XML_V1.java b/src/jalview/gui/Jalview2XML_V1.java index 586e2fa..cc2f636 100755 --- a/src/jalview/gui/Jalview2XML_V1.java +++ b/src/jalview/gui/Jalview2XML_V1.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2) - * Copyright (C) 2014 The Jalview Authors + * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) + * Copyright (C) $$Year-Rel$$ The Jalview Authors * * This file is part of Jalview. * @@ -20,6 +20,7 @@ */ package jalview.gui; +import jalview.analysis.Conservation; import jalview.binding.Annotation; import jalview.binding.AnnotationElement; import jalview.binding.Features; @@ -34,24 +35,23 @@ import jalview.binding.Setting; import jalview.binding.Tree; import jalview.binding.UserColours; import jalview.binding.Viewport; +import jalview.datamodel.PDBEntry; +import jalview.io.FileFormat; import jalview.schemes.ColourSchemeI; import jalview.schemes.ColourSchemeProperty; -import jalview.schemes.ResidueProperties; import jalview.structure.StructureSelectionManager; import jalview.util.MessageManager; import jalview.util.jarInputStreamProvider; import jalview.viewmodel.seqfeatures.FeatureRendererSettings; import java.io.InputStreamReader; +import java.io.Reader; +import java.net.UnknownHostException; import java.util.Hashtable; import java.util.Vector; import java.util.jar.JarEntry; import java.util.jar.JarInputStream; -import javax.swing.JOptionPane; - -import org.exolab.castor.xml.IDResolver; - /** * DOCUMENT ME! * @@ -126,44 +126,39 @@ public class Jalview2XML_V1 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(); + entryCount++; + if (jarentry.getName().endsWith(".xml")) + { + Reader in = new InputStreamReader(jin, "UTF-8"); + JalviewModel object = new JalviewModel(); - object = object.unmarshal(in); + object = object.unmarshal(in); - af = LoadFromObject(object, file); - entryCount++; + af = LoadFromObject(object, file); + } } + jin.close(); } while (jarentry != null); - } catch (final java.net.UnknownHostException ex) + } catch (final UnknownHostException ex) { ex.printStackTrace(); if (raiseGUI) { javax.swing.SwingUtilities.invokeLater(new Runnable() { + @Override public void run() { System.err.println("Couldn't locate Jalview XML file : " + ex + "\n"); - JOptionPane.showInternalMessageDialog(Desktop.desktop, + JvOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager.formatMessage("label.couldnt_locate", - new String[] - { file }), MessageManager + new String[] { file }), MessageManager .getString("label.url_not_found"), - JOptionPane.WARNING_MESSAGE); + JvOptionPane.WARNING_MESSAGE); } }); } @@ -176,12 +171,16 @@ public class Jalview2XML_V1 { javax.swing.SwingUtilities.invokeLater(new Runnable() { + @Override public void run() { - JOptionPane.showInternalMessageDialog(Desktop.desktop, - MessageManager.formatMessage("label.error_loading_file_params", new String[]{file}), MessageManager.getString("label.error_loading_jalview_file"), - JOptionPane.WARNING_MESSAGE); + JvOptionPane.showInternalMessageDialog(Desktop.desktop, + MessageManager.formatMessage( + "label.error_loading_file_params", new String[] + { file }), MessageManager + .getString("label.error_loading_jalview_file"), + JvOptionPane.WARNING_MESSAGE); } }); } @@ -240,7 +239,17 @@ public class Jalview2XML_V1 { jalview.datamodel.PDBEntry entry = new jalview.datamodel.PDBEntry(); entry.setId(ids[p].getId()); - entry.setType(ids[p].getType()); + if (ids[p].getType() != null) + { + if (ids[p].getType().equalsIgnoreCase("PDB")) + { + entry.setType(PDBEntry.Type.PDB); + } + else + { + entry.setType(PDBEntry.Type.FILE); + } + } al.getSequenceAt(i).getDatasetSequence().addPDBId(entry); StructureSelectionManager.getStructureSelectionManager( Desktop.instance).registerPDBEntry(entry); @@ -295,7 +304,7 @@ public class Jalview2XML_V1 AlignFrame af = new AlignFrame(al, view.getWidth(), view.getHeight()); - af.setFileName(file, "Jalview"); + af.setFileName(file, FileFormat.Jalview); for (int i = 0; i < JSEQ.length; i++) { @@ -322,37 +331,31 @@ public class Jalview2XML_V1 } else { - cs = ColourSchemeProperty.getColour(al, groups[i].getColour()); - } - - if (cs != null) - { - cs.setThreshold(groups[i].getPidThreshold(), true); + cs = ColourSchemeProperty.getColourScheme(al, groups[i].getColour()); } - } + int pidThreshold = groups[i].getPidThreshold(); Vector seqs = new Vector(); int[] ids = groups[i].getSeq(); for (int s = 0; s < ids.length; s++) { - seqs.addElement(seqids - .elementAt(ids[s])); + seqs.addElement(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.getGroupColourScheme().setThreshold(pidThreshold, true); 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.getSequences(null), 0, sg.getWidth() - 1); + Conservation c = new Conservation("All", sg.getSequences(null), + 0, sg.getWidth() - 1); c.calculate(); c.verdict(false, 25); sg.cs.setConservation(c); @@ -364,22 +367,21 @@ public class Jalview2XML_V1 af.setBounds(view.getXpos(), view.getYpos(), view.getWidth(), view.getHeight()); - af.viewport.setStartRes(view.getStartRes()); - af.viewport.setStartSeq(view.getStartSeq()); + af.viewport.getRanges().setStartRes(view.getStartRes()); + af.viewport.getRanges().setStartSeq(view.getStartSeq()); af.viewport.setShowAnnotation(view.getShowAnnotation()); af.viewport.setAbovePIDThreshold(view.getPidSelected()); af.viewport.setColourText(view.getShowColourText()); af.viewport.setConservationSelected(view.getConservationSelected()); af.viewport.setShowJVSuffix(view.getShowFullId()); - af.viewport.setFont(new java.awt.Font(view.getFontName(), view - .getFontStyle(), view.getFontSize())); - af.alignPanel.fontChanged(); + af.viewport.setFont( + new java.awt.Font(view.getFontName(), view.getFontStyle(), view + .getFontSize()), true); af.viewport.setRenderGaps(view.getRenderGaps()); af.viewport.setWrapAlignment(view.getWrapAlignment()); - af.alignPanel.setWrapAlignment(view.getWrapAlignment()); - af.viewport.setShowAnnotation(view.getShowAnnotation()); - af.alignPanel.setAnnotationVisible(view.getShowAnnotation()); + + af.viewport.setShowAnnotation(view.isShowAnnotation()); af.viewport.setShowBoxes(view.getShowBoxes()); af.viewport.setShowText(view.getShowText()); @@ -393,22 +395,27 @@ public class Jalview2XML_V1 } else { - cs = ColourSchemeProperty.getColour(al, view.getBgColour()); + cs = ColourSchemeProperty.getColourScheme(al, view.getBgColour()); } - if (cs != null) - { - cs.setThreshold(view.getPidThreshold(), true); - cs.setConsensus(af.viewport.getSequenceConsensusHash()); - } + // if (cs != null) + // { + // cs.setThreshold(view.getPidThreshold(), true); + // cs.setConsensus(af.viewport.getSequenceConsensusHash()); + // } } - af.viewport.setGlobalColourScheme(cs); + af.viewport.getResidueShading().setThreshold( + view.getPidThreshold(), true); + af.viewport.getResidueShading().setConsensus( + af.viewport.getSequenceConsensusHash()); af.viewport.setColourAppliesToAllGroups(false); + af.alignPanel.updateLayout(); af.changeColour(cs); if (view.getConservationSelected() && cs != null) { - cs.setConservationInc(view.getConsThreshold()); + af.viewport.getResidueShading().setConservationInc( + view.getConsThreshold()); } af.viewport.setColourAppliesToAllGroups(true); @@ -424,19 +431,21 @@ public class Jalview2XML_V1 { Setting setting = jms.getFeatureSettings().getSetting(fs); - featureColours.put( - setting.getType(), new java.awt.Color(setting.getColour())); + featureColours.put(setting.getType(), + new java.awt.Color(setting.getColour())); renderOrder[fs] = setting.getType(); if (setting.getDisplay()) { - featuresDisplayed.put(setting.getType(), new Integer( - setting.getColour())); + featuresDisplayed.put(setting.getType(), + new Integer(setting.getColour())); } } - FeatureRendererSettings frs = new FeatureRendererSettings(renderOrder, new Hashtable(), featureColours, 1.0f, null); - af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer().transferSettings(frs); + FeatureRendererSettings frs = new FeatureRendererSettings( + renderOrder, new Hashtable(), featureColours, 1.0f, null); + af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer() + .transferSettings(frs); } af.setMenusFromViewport(af.viewport); @@ -455,7 +464,7 @@ public class Jalview2XML_V1 Tree tree = jms.getTree(t); - TreePanel tp = af.ShowNewickTree( + TreePanel tp = af.showNewickTree( new jalview.io.NewickFile(tree.getNewick()), tree.getTitle(), tree.getWidth(), tree.getHeight(), tree.getXpos(), tree.getYpos());