X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FJalview2XML_V1.java;h=9548839f83b633286676dc8f609fef3a1462ab5c;hb=7e82e1fed011077e5cd4cc40ac8ad3519d7c47a8;hp=aefc233db286d963a1e691ca96703df912a40637;hpb=320c96aed11f5c396a9efd9ea83b0e35f05e21e4;p=jalview.git diff --git a/src/jalview/gui/Jalview2XML_V1.java b/src/jalview/gui/Jalview2XML_V1.java index aefc233..9548839 100755 --- a/src/jalview/gui/Jalview2XML_V1.java +++ b/src/jalview/gui/Jalview2XML_V1.java @@ -36,6 +36,7 @@ import jalview.binding.Tree; import jalview.binding.UserColours; import jalview.binding.Viewport; import jalview.datamodel.PDBEntry; +import jalview.datamodel.SequenceFeature; import jalview.io.FileFormat; import jalview.schemes.ColourSchemeI; import jalview.schemes.ColourSchemeProperty; @@ -52,8 +53,6 @@ import java.util.Vector; import java.util.jar.JarEntry; import java.util.jar.JarInputStream; -import javax.swing.JOptionPane; - /** * DOCUMENT ME! * @@ -95,8 +94,8 @@ public class Jalview2XML_V1 for (int i = 0; i < csize; i++) { - newColours[i] = new java.awt.Color(Integer.parseInt(colours - .getUserColourScheme().getColour(i).getRGB(), 16)); + newColours[i] = new java.awt.Color(Integer.parseInt( + colours.getUserColourScheme().getColour(i).getRGB(), 16)); } return new jalview.schemes.UserColourScheme(newColours); @@ -154,12 +153,13 @@ public class Jalview2XML_V1 public void run() { - System.err.println("Couldn't locate Jalview XML file : " + ex - + "\n"); + System.err.println( + "Couldn't locate Jalview XML file : " + ex + "\n"); JvOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager.formatMessage("label.couldnt_locate", - new String[] { file }), MessageManager - .getString("label.url_not_found"), + new String[] + { file }), + MessageManager.getString("label.url_not_found"), JvOptionPane.WARNING_MESSAGE); } }); @@ -180,7 +180,8 @@ public class Jalview2XML_V1 JvOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager.formatMessage( "label.error_loading_file_params", new String[] - { file }), MessageManager + { file }), + MessageManager .getString("label.error_loading_jalview_file"), JvOptionPane.WARNING_MESSAGE); } @@ -226,11 +227,10 @@ public class Jalview2XML_V1 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(), + SequenceFeature sf = new SequenceFeature(features[f].getType(), + features[f].getDescription(), features[f].getBegin(), features[f].getEnd(), null); - + sf.setStatus(features[f].getStatus()); al.getSequenceAt(i).getDatasetSequence().addSequenceFeature(sf); } } @@ -253,8 +253,9 @@ public class Jalview2XML_V1 } } al.getSequenceAt(i).getDatasetSequence().addPDBId(entry); - StructureSelectionManager.getStructureSelectionManager( - Desktop.instance).registerPDBEntry(entry); + StructureSelectionManager + .getStructureSelectionManager(Desktop.instance) + .registerPDBEntry(entry); } } @@ -310,8 +311,9 @@ public class Jalview2XML_V1 for (int i = 0; i < JSEQ.length; i++) { - af.viewport.setSequenceColour(af.viewport.getAlignment() - .getSequenceAt(i), new java.awt.Color(JSEQ[i].getColour())); + af.viewport.setSequenceColour( + af.viewport.getAlignment().getSequenceAt(i), + new java.awt.Color(JSEQ[i].getColour())); } // af.changeColour() ); @@ -333,15 +335,11 @@ public class Jalview2XML_V1 } else { - cs = ColourSchemeProperty.getColourScheme(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(); @@ -355,13 +353,15 @@ public class Jalview2XML_V1 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())); + sg.setOutlineColour( + new java.awt.Color(groups[i].getOutlineColour())); if (groups[i].getConsThreshold() != 0) { - Conservation c = new Conservation("All", 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); @@ -373,16 +373,15 @@ 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()); + // startSeq set in af.alignPanel.updateLayout below 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()), true); + af.viewport.setFont(new java.awt.Font(view.getFontName(), + view.getFontStyle(), view.getFontSize()), true); af.viewport.setRenderGaps(view.getRenderGaps()); af.viewport.setWrapAlignment(view.getWrapAlignment()); @@ -404,20 +403,24 @@ public class Jalview2XML_V1 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); @@ -429,7 +432,8 @@ public class Jalview2XML_V1 Hashtable featureColours = new Hashtable(); String[] renderOrder = new String[jms.getFeatureSettings() .getSettingCount()]; - for (int fs = 0; fs < jms.getFeatureSettings().getSettingCount(); fs++) + for (int fs = 0; fs < jms.getFeatureSettings() + .getSettingCount(); fs++) { Setting setting = jms.getFeatureSettings().getSetting(fs); @@ -444,8 +448,8 @@ public class Jalview2XML_V1 new Integer(setting.getColour())); } } - FeatureRendererSettings frs = new FeatureRendererSettings( - renderOrder, new Hashtable(), featureColours, 1.0f, null); + FeatureRendererSettings frs = new FeatureRendererSettings(renderOrder, + new Hashtable(), featureColours, 1.0f, null); af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer() .transferSettings(frs); } @@ -466,7 +470,7 @@ 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()); @@ -476,20 +480,20 @@ public class Jalview2XML_V1 if (tree.getFontName() != null) { - tp.setTreeFont(new java.awt.Font(tree.getFontName(), tree - .getFontStyle(), tree.getFontSize())); + 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.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(); + tp.getTreeCanvas().setThreshold(tree.getThreshold()); if (tree.getCurrentTree()) {