X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FJalview2XML.java;h=55d29d514fd6e0997df57a344edb5e965070e601;hb=d559b47886de6427219011e6e355320a0babd757;hp=a4e5785a1a57c310e6bc0aa4d1c8c4d05d7f2d68;hpb=296572df6fc3100c1fd97f3714bb2b6628140310;p=jalview.git diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java index a4e5785..55d29d5 100644 --- a/src/jalview/gui/Jalview2XML.java +++ b/src/jalview/gui/Jalview2XML.java @@ -37,6 +37,9 @@ import jalview.datamodel.StructureViewerModel; import jalview.datamodel.StructureViewerModel.StructureData; import jalview.ext.varna.RnaModel; import jalview.gui.StructureViewer.ViewerType; +import jalview.io.DataSourceType; +import jalview.io.FileFormat; +import jalview.renderer.ResidueShaderI; import jalview.schemabinding.version2.AlcodMap; import jalview.schemabinding.version2.AlcodonFrame; import jalview.schemabinding.version2.Annotation; @@ -127,7 +130,6 @@ 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.Marshaller; @@ -992,17 +994,16 @@ public class Jalview2XML } } - if (entry.getProperty() != null && !entry.getProperty().isEmpty()) + Enumeration props = entry.getProperties(); + if (props.hasMoreElements()) { PdbentryItem item = new PdbentryItem(); - Hashtable properties = entry.getProperty(); - Enumeration en2 = properties.keys(); - while (en2.hasMoreElements()) + while (props.hasMoreElements()) { Property prop = new Property(); - String key = en2.nextElement().toString(); + String key = props.nextElement(); prop.setName(key); - prop.setValue(properties.get(key).toString()); + prop.setValue(entry.getProperty(key).toString()); item.addProperty(prop); } pdb.addPdbentryItem(item); @@ -1174,38 +1175,43 @@ public class Jalview2XML // group has references so set its ID field jGroup.setId(groupRefs.get(sg)); } - if (sg.cs != null) + ColourSchemeI colourScheme = sg.getColourScheme(); + if (colourScheme != null) { - if (sg.cs.conservationApplied()) + ResidueShaderI groupColourScheme = sg + .getGroupColourScheme(); + if (groupColourScheme.conservationApplied()) { - jGroup.setConsThreshold(sg.cs.getConservationInc()); + jGroup.setConsThreshold(groupColourScheme.getConservationInc()); - if (sg.cs instanceof jalview.schemes.UserColourScheme) + if (colourScheme instanceof jalview.schemes.UserColourScheme) { - jGroup.setColour(setUserColourScheme(sg.cs, userColours, jms)); + jGroup.setColour(setUserColourScheme(colourScheme, + userColours, jms)); } else { - jGroup.setColour(ColourSchemeProperty.getColourName(sg.cs)); + jGroup.setColour(colourScheme.getSchemeName()); } } - else if (sg.cs instanceof jalview.schemes.AnnotationColourGradient) + else if (colourScheme instanceof jalview.schemes.AnnotationColourGradient) { jGroup.setColour("AnnotationColourGradient"); jGroup.setAnnotationColours(constructAnnotationColours( - (jalview.schemes.AnnotationColourGradient) sg.cs, + (jalview.schemes.AnnotationColourGradient) colourScheme, userColours, jms)); } - else if (sg.cs instanceof jalview.schemes.UserColourScheme) + else if (colourScheme instanceof jalview.schemes.UserColourScheme) { - jGroup.setColour(setUserColourScheme(sg.cs, userColours, jms)); + jGroup.setColour(setUserColourScheme(colourScheme, + userColours, jms)); } else { - jGroup.setColour(ColourSchemeProperty.getColourName(sg.cs)); + jGroup.setColour(colourScheme.getSchemeName()); } - jGroup.setPidThreshold(sg.cs.getThreshold()); + jGroup.setPidThreshold(groupColourScheme.getThreshold()); } jGroup.setOutlineColour(sg.getOutlineColour().getRGB()); @@ -1264,8 +1270,8 @@ public class Jalview2XML view.setWidth(size.width); view.setHeight(size.height); - view.setStartRes(av.startRes); - view.setStartSeq(av.startSeq); + view.setStartRes(av.getStartRes()); + view.setStartSeq(av.getStartSeq()); if (av.getGlobalColourScheme() instanceof jalview.schemes.UserColourScheme) { @@ -1288,23 +1294,20 @@ public class Jalview2XML .getGlobalColourScheme())); } + ResidueShaderI vcs = av.getResidueShading(); ColourSchemeI cs = av.getGlobalColourScheme(); if (cs != null) { - if (cs.conservationApplied()) + if (vcs.conservationApplied()) { - view.setConsThreshold(cs.getConservationInc()); + view.setConsThreshold(vcs.getConservationInc()); if (cs instanceof jalview.schemes.UserColourScheme) { view.setBgColour(setUserColourScheme(cs, userColours, jms)); } } - - if (cs instanceof ResidueColourScheme) - { - view.setPidThreshold(cs.getThreshold()); - } + view.setPidThreshold(vcs.getThreshold()); } view.setConservationSelected(av.getConservationSelected()); @@ -1723,8 +1726,7 @@ public class Jalview2XML } else { - ac.setColourScheme(ColourSchemeProperty.getColourName(acg - .getBaseColour())); + ac.setColourScheme(ColourSchemeProperty.getColourName(acg.getBaseColour())); } ac.setMaxColour(acg.getMaxColour().getRGB()); @@ -2637,10 +2639,10 @@ public class Jalview2XML @Override public void run() { - JOptionPane.showInternalMessageDialog(Desktop.desktop, + JvOptionPane.showInternalMessageDialog(Desktop.desktop, finalErrorMessage, "Error " + (saving ? "saving" : "loading") - + " Jalview file", JOptionPane.WARNING_MESSAGE); + + " Jalview file", JvOptionPane.WARNING_MESSAGE); } }); } @@ -3033,12 +3035,11 @@ public class Jalview2XML } if (ids[p].getPdbentryItem() != null) { - entry.setProperty(new Hashtable()); for (PdbentryItem item : ids[p].getPdbentryItem()) { for (Property pr : item.getProperty()) { - entry.getProperty().put(pr.getName(), pr.getValue()); + entry.setProperty(pr.getName(), pr.getValue()); } } } @@ -3342,18 +3343,13 @@ public class Jalview2XML && jGroup.getAnnotationColours() != null) { addAnnotSchemeGroup = true; - cs = null; } else { - cs = ColourSchemeProperty.getColour(al, jGroup.getColour()); - } - - if (cs != null) - { - cs.setThreshold(jGroup.getPidThreshold(), true); + cs = ColourSchemeProperty.getColourScheme(al, jGroup.getColour()); } } + int pidThreshold = jGroup.getPidThreshold(); Vector seqs = new Vector(); @@ -3376,7 +3372,8 @@ public class Jalview2XML SequenceGroup sg = new SequenceGroup(seqs, jGroup.getName(), cs, jGroup.getDisplayBoxes(), jGroup.getDisplayText(), jGroup.getColourText(), jGroup.getStart(), jGroup.getEnd()); - + sg.getGroupColourScheme().setThreshold(pidThreshold, true); + sg.getGroupColourScheme().setConservationInc(jGroup.getConsThreshold()); sg.setOutlineColour(new java.awt.Color(jGroup.getOutlineColour())); sg.textColour = new java.awt.Color(jGroup.getTextCol1()); @@ -3403,8 +3400,8 @@ public class Jalview2XML } if (jGroup.getConsThreshold() != 0) { - Conservation c = new Conservation("All", 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); @@ -3442,8 +3439,8 @@ public class Jalview2XML if (addAnnotSchemeGroup) { // reconstruct the annotation colourscheme - sg.cs = constructAnnotationColour(jGroup.getAnnotationColours(), - null, al, jms, false); + sg.setColourScheme(constructAnnotationColour( + jGroup.getAnnotationColours(), null, al, jms, false)); } } } @@ -4232,8 +4229,7 @@ public class Jalview2XML StructureData filedat = oldFiles.get(id); String pdbFile = filedat.getFilePath(); SequenceI[] seq = filedat.getSeqList().toArray(new SequenceI[0]); - binding.getSsm().setMapping(seq, null, pdbFile, - jalview.io.AppletFormatAdapter.FILE); + binding.getSsm().setMapping(seq, null, pdbFile, DataSourceType.FILE); binding.addSequenceForStructFile(pdbFile, seq); } // and add the AlignmentPanel's reference to the view panel @@ -4348,7 +4344,7 @@ public class Jalview2XML af = new AlignFrame(al, view.getWidth(), view.getHeight(), uniqueSeqSetId, viewId); - af.setFileName(file, "Jalview"); + af.setFileName(file, FileFormat.Jalview); for (int i = 0; i < JSEQ.length; i++) { @@ -4423,10 +4419,12 @@ public class Jalview2XML af.viewport.setShowAnnotation(view.getShowAnnotation()); af.viewport.setAbovePIDThreshold(view.getPidSelected()); + af.viewport.setThreshold(view.getPidThreshold()); af.viewport.setColourText(view.getShowColourText()); af.viewport.setConservationSelected(view.getConservationSelected()); + af.viewport.setIncrement(view.getConsThreshold()); af.viewport.setShowJVSuffix(view.getShowFullId()); af.viewport.setRightAlignIds(view.getRightAlignIds()); af.viewport.setFont( @@ -4471,22 +4469,21 @@ public class Jalview2XML } else { - cs = ColourSchemeProperty.getColour(al, view.getBgColour()); - } - - if (cs != null) - { - cs.setThreshold(view.getPidThreshold(), true); - cs.setConsensus(af.viewport.getSequenceConsensusHash()); + cs = ColourSchemeProperty.getColourScheme(al, view.getBgColour()); } } af.viewport.setGlobalColourScheme(cs); + af.viewport.getResidueShading().setThreshold( + view.getPidThreshold(), true); + af.viewport.getResidueShading().setConsensus( + af.viewport.getSequenceConsensusHash()); af.viewport.setColourAppliesToAllGroups(false); if (view.getConservationSelected() && cs != null) { - cs.setConservationInc(view.getConsThreshold()); + af.viewport.getResidueShading().setConservationInc( + view.getConsThreshold()); } af.changeColour(cs); @@ -4707,7 +4704,7 @@ public class Jalview2XML propagateAnnColour = true; for (jalview.datamodel.SequenceGroup sg : al.getGroups()) { - if (sg.cs instanceof AnnotationColourGradient) + if (sg.getColourScheme() instanceof AnnotationColourGradient) { propagateAnnColour = false; } @@ -4731,7 +4728,8 @@ public class Jalview2XML ); } - if (viewAnnColour.getColourScheme().equals("None")) + if (viewAnnColour.getColourScheme().equals( + ResidueColourScheme.NONE)) { cs = new AnnotationColourGradient( annAlignment.getAlignmentAnnotation()[i], @@ -4751,7 +4749,7 @@ public class Jalview2XML { cs = new AnnotationColourGradient( annAlignment.getAlignmentAnnotation()[i], - ColourSchemeProperty.getColour(al, + ColourSchemeProperty.getColourScheme(al, viewAnnColour.getColourScheme()), viewAnnColour.getAboveThreshold()); } @@ -4779,7 +4777,7 @@ public class Jalview2XML } /* - * if (viewAnnColour.getColourScheme().equals("None" )) { sg.cs = + * if (viewAnnColour.getColourScheme().equals(ResidueColourScheme.NONE)) { sg.cs = * new AnnotationColourGradient( * annAlignment.getAlignmentAnnotation()[i], new * java.awt.Color(viewAnnColour. getMinColour()), new @@ -4787,9 +4785,10 @@ public class Jalview2XML * viewAnnColour.getAboveThreshold()); } else */ { - sg.cs = new AnnotationColourGradient( - annAlignment.getAlignmentAnnotation()[i], sg.cs, - viewAnnColour.getAboveThreshold()); + sg.setColourScheme(new AnnotationColourGradient( + annAlignment.getAlignmentAnnotation()[i], sg + .getColourScheme(), viewAnnColour + .getAboveThreshold())); if (cs instanceof AnnotationColourGradient) { if (viewAnnColour.hasPerSequence())