From 3325395b33ef3b52b4a62327621c5bddf12ee4e0 Mon Sep 17 00:00:00 2001 From: Jim Procter Date: Thu, 30 Oct 2014 15:21:31 +0000 Subject: [PATCH] JAL-1551 format and tidy --- src/MCview/PDBfile.java | 23 ++-- src/jalview/appletgui/AlignFrame.java | 32 +++++- src/jalview/bin/JalviewLite.java | 4 + src/jalview/ext/jmol/PDBFileWithJmol.java | 25 ++-- src/jalview/gui/AlignFrame.java | 46 ++++++++ src/jalview/gui/Jalview2XML.java | 119 +++++++++++++++++--- src/jalview/gui/Jalview2XML_V1.java | 41 +++++-- src/jalview/io/FileLoader.java | 3 +- .../structure/StructureSelectionManager.java | 6 +- 9 files changed, 245 insertions(+), 54 deletions(-) diff --git a/src/MCview/PDBfile.java b/src/MCview/PDBfile.java index a99f172..7d2ceac 100755 --- a/src/MCview/PDBfile.java +++ b/src/MCview/PDBfile.java @@ -33,11 +33,12 @@ import java.awt.Color; import java.io.IOException; import java.util.ArrayList; import java.util.Hashtable; +import java.util.List; import java.util.Vector; public class PDBfile extends jalview.io.AlignFile { - public Vector chains; + public Vector chains; public String id; @@ -181,15 +182,15 @@ public class PDBfile extends jalview.io.AlignFile } for (int i = 0; i < chains.size(); i++) { - SequenceI dataset = ((PDBChain) chains.elementAt(i)).sequence; + SequenceI dataset = chains.elementAt(i).sequence; dataset.setName(id + "|" + dataset.getName()); PDBEntry entry = new PDBEntry(); entry.setId(id); entry.setProperty(new Hashtable()); - if (((PDBChain) chains.elementAt(i)).id != null) + if (chains.elementAt(i).id != null) { entry.getProperty().put("CHAIN", - ((PDBChain) chains.elementAt(i)).id); + chains.elementAt(i).id); } if (inFile != null) { @@ -406,7 +407,7 @@ public class PDBfile extends jalview.io.AlignFile { for (int i = 0; i < chains.size(); i++) { - ((PDBChain) chains.elementAt(i)).makeResidueList(); + chains.elementAt(i).makeResidueList(); } } @@ -414,7 +415,7 @@ public class PDBfile extends jalview.io.AlignFile { for (int i = 0; i < chains.size(); i++) { - ((PDBChain) chains.elementAt(i)).makeCaBondList(); + chains.elementAt(i).makeCaBondList(); } } @@ -422,9 +423,9 @@ public class PDBfile extends jalview.io.AlignFile { for (int i = 0; i < chains.size(); i++) { - if (((PDBChain) chains.elementAt(i)).id.equals(id)) + if (chains.elementAt(i).id.equals(id)) { - return (PDBChain) chains.elementAt(i); + return chains.elementAt(i); } } @@ -435,7 +436,7 @@ public class PDBfile extends jalview.io.AlignFile { for (int i = 0; i < chains.size(); i++) { - ((PDBChain) chains.elementAt(i)).setChargeColours(); + chains.elementAt(i).setChargeColours(); } } @@ -443,7 +444,7 @@ public class PDBfile extends jalview.io.AlignFile { for (int i = 0; i < chains.size(); i++) { - ((PDBChain) chains.elementAt(i)).setChainColours(cs); + chains.elementAt(i).setChainColours(cs); } } @@ -451,7 +452,7 @@ public class PDBfile extends jalview.io.AlignFile { for (int i = 0; i < chains.size(); i++) { - ((PDBChain) chains.elementAt(i)).setChainColours(Color.getHSBColor( + chains.elementAt(i).setChainColours(Color.getHSBColor( 1.0f / i, .4f, 1.0f)); } } diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java index f267858..8449a53 100644 --- a/src/jalview/appletgui/AlignFrame.java +++ b/src/jalview/appletgui/AlignFrame.java @@ -21,7 +21,6 @@ package jalview.appletgui; import jalview.analysis.AlignmentSorter; -import jalview.analysis.Conservation; import jalview.api.AlignViewControllerGuiI; import jalview.api.AlignViewControllerI; import jalview.api.SequenceStructureBinding; @@ -56,7 +55,6 @@ import jalview.schemes.PIDColourScheme; import jalview.schemes.PurinePyrimidineColourScheme; import jalview.schemes.RNAHelicesColourChooser; import jalview.schemes.RNAInteractionColourScheme; -import jalview.schemes.ResidueProperties; import jalview.schemes.StrandColourScheme; import jalview.schemes.TCoffeeColourScheme; import jalview.schemes.TaylorColourScheme; @@ -324,7 +322,9 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, .getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt .getKeyCode() <= KeyEvent.VK_NUMPAD9)) && Character.isDigit(evt.getKeyChar())) + { alignPanel.seqPanel.numberPressed(evt.getKeyChar()); + } switch (evt.getKeyCode()) { @@ -385,16 +385,24 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, case KeyEvent.VK_LEFT: if (evt.isAltDown() || !viewport.cursorMode) + { slideSequences(false, alignPanel.seqPanel.getKeyboardNo1()); + } else + { alignPanel.seqPanel.moveCursor(-1, 0); + } break; case KeyEvent.VK_RIGHT: if (evt.isAltDown() || !viewport.cursorMode) + { slideSequences(true, alignPanel.seqPanel.getKeyboardNo1()); + } else + { alignPanel.seqPanel.moveCursor(1, 0); + } break; case KeyEvent.VK_SPACE: @@ -1257,7 +1265,9 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, else { if (features == null) + { features = ""; + } } return features; @@ -1573,7 +1583,9 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, for (int i = 0; i < viewport.getAlignment().getHeight(); i++) { if (!sg.contains(viewport.getAlignment().getSequenceAt(i))) + { invertGroup.addElement(viewport.getAlignment().getSequenceAt(i)); + } } SequenceI[] seqs1 = sg.toArray(new SequenceI[sg.size()]); @@ -1581,30 +1593,44 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, SequenceI[] seqs2 = invertGroup.toArray(new SequenceI[invertGroup .size()]); for (int i = 0; i < invertGroup.size(); i++) + { seqs2[i] = invertGroup.elementAt(i); + } SlideSequencesCommand ssc; if (right) + { ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1, size, viewport.getGapCharacter()); + } else + { ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2, size, viewport.getGapCharacter()); + } int groupAdjustment = 0; if (ssc.getGapsInsertedBegin() && right) { if (viewport.cursorMode) + { alignPanel.seqPanel.moveCursor(size, 0); + } else + { groupAdjustment = size; + } } else if (!ssc.getGapsInsertedBegin() && !right) { if (viewport.cursorMode) + { alignPanel.seqPanel.moveCursor(-size, 0); + } else + { groupAdjustment = -size; + } } if (groupAdjustment != 0) @@ -1625,7 +1651,9 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, } if (!appendHistoryItem) + { addHistoryItem(ssc); + } repaint(); } diff --git a/src/jalview/bin/JalviewLite.java b/src/jalview/bin/JalviewLite.java index ef1e16e..d3f03be 100644 --- a/src/jalview/bin/JalviewLite.java +++ b/src/jalview/bin/JalviewLite.java @@ -2076,10 +2076,12 @@ public class JalviewLite extends Applet implements { String sequence = applet.getParameter("PDBSEQ"); if (sequence != null) + { seqs = new SequenceI[] { matcher == null ? (Sequence) newAlignFrame .getAlignViewport().getAlignment() .findName(sequence) : matcher.findIdMatch(sequence) }; + } } else @@ -2323,7 +2325,9 @@ public class JalviewLite extends Applet implements // note separator local variable intentionally masks object field int seplen = separator.length(); if (list == null || list.equals("") || list.equals(separator)) + { return null; + } java.util.Vector jv = new Vector(); int cp = 0, pos; while ((pos = list.indexOf(separator, cp)) > cp) diff --git a/src/jalview/ext/jmol/PDBFileWithJmol.java b/src/jalview/ext/jmol/PDBFileWithJmol.java index 847453f..159955a 100644 --- a/src/jalview/ext/jmol/PDBFileWithJmol.java +++ b/src/jalview/ext/jmol/PDBFileWithJmol.java @@ -20,6 +20,15 @@ */ package jalview.ext.jmol; +import jalview.datamodel.AlignmentAnnotation; +import jalview.datamodel.Annotation; +import jalview.datamodel.PDBEntry; +import jalview.datamodel.Sequence; +import jalview.datamodel.SequenceI; +import jalview.io.AlignFile; +import jalview.io.FileParse; +import jalview.util.MessageManager; + import java.io.IOException; import java.util.Hashtable; import java.util.Map; @@ -35,15 +44,6 @@ import org.jmol.modelsetbio.BioPolymer; import org.jmol.viewer.Viewer; import org.openscience.jmol.app.JmolApp; -import jalview.datamodel.AlignmentAnnotation; -import jalview.datamodel.Annotation; -import jalview.datamodel.PDBEntry; -import jalview.datamodel.Sequence; -import jalview.datamodel.SequenceI; -import jalview.io.AlignFile; -import jalview.io.FileParse; -import jalview.util.MessageManager; - /** * Import and process PDB files with Jmol * @@ -307,11 +307,16 @@ public class PDBFileWithJmol extends AlignFile implements case MEASURE: String mystatus = (String) data[3]; if (mystatus.indexOf("Picked") >= 0 - || mystatus.indexOf("Sequence") >= 0) // picking mode + || mystatus.indexOf("Sequence") >= 0) + { + // Picking mode sendConsoleMessage(strInfo); + } else if (mystatus.indexOf("Completed") >= 0) + { sendConsoleEcho(strInfo.substring(strInfo.lastIndexOf(",") + 2, strInfo.length() - 1)); + } break; case MESSAGE: sendConsoleMessage(data == null ? null : strInfo); diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java index d9c0c6a..6b4aa1f 100644 --- a/src/jalview/gui/AlignFrame.java +++ b/src/jalview/gui/AlignFrame.java @@ -377,7 +377,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, .getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt .getKeyCode() <= KeyEvent.VK_NUMPAD9)) && Character.isDigit(evt.getKeyChar())) + { alignPanel.seqPanel.numberPressed(evt.getKeyChar()); + } switch (evt.getKeyCode()) { @@ -389,32 +391,48 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, case KeyEvent.VK_DOWN: if (evt.isAltDown() || !viewport.cursorMode) + { moveSelectedSequences(false); + } if (viewport.cursorMode) + { alignPanel.seqPanel.moveCursor(0, 1); + } break; case KeyEvent.VK_UP: if (evt.isAltDown() || !viewport.cursorMode) + { moveSelectedSequences(true); + } if (viewport.cursorMode) + { alignPanel.seqPanel.moveCursor(0, -1); + } break; case KeyEvent.VK_LEFT: if (evt.isAltDown() || !viewport.cursorMode) + { slideSequences(false, alignPanel.seqPanel.getKeyboardNo1()); + } else + { alignPanel.seqPanel.moveCursor(-1, 0); + } break; case KeyEvent.VK_RIGHT: if (evt.isAltDown() || !viewport.cursorMode) + { slideSequences(true, alignPanel.seqPanel.getKeyboardNo1()); + } else + { alignPanel.seqPanel.moveCursor(1, 0); + } break; case KeyEvent.VK_SPACE: @@ -551,14 +569,18 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { case KeyEvent.VK_LEFT: if (evt.isAltDown() || !viewport.cursorMode) + { viewport.firePropertyChange("alignment", null, viewport .getAlignment().getSequences()); + } break; case KeyEvent.VK_RIGHT: if (evt.isAltDown() || !viewport.cursorMode) + { viewport.firePropertyChange("alignment", null, viewport .getAlignment().getSequences()); + } break; } } @@ -1458,7 +1480,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, protected void undoMenuItem_actionPerformed(ActionEvent e) { if (viewport.historyList.empty()) + { return; + } CommandI command = (CommandI) viewport.historyList.pop(); viewport.redoList.push(command); command.undoCommand(getViewAlignments()); @@ -1611,37 +1635,53 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, for (int i = 0; i < viewport.getAlignment().getHeight(); i++) { if (!sg.contains(viewport.getAlignment().getSequenceAt(i))) + { invertGroup.add(viewport.getAlignment().getSequenceAt(i)); + } } SequenceI[] seqs1 = sg.toArray(new SequenceI[0]); SequenceI[] seqs2 = new SequenceI[invertGroup.size()]; for (int i = 0; i < invertGroup.size(); i++) + { seqs2[i] = (SequenceI) invertGroup.elementAt(i); + } SlideSequencesCommand ssc; if (right) + { ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1, size, viewport.getGapCharacter()); + } else + { ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2, size, viewport.getGapCharacter()); + } int groupAdjustment = 0; if (ssc.getGapsInsertedBegin() && right) { if (viewport.cursorMode) + { alignPanel.seqPanel.moveCursor(size, 0); + } else + { groupAdjustment = size; + } } else if (!ssc.getGapsInsertedBegin() && !right) { if (viewport.cursorMode) + { alignPanel.seqPanel.moveCursor(-size, 0); + } else + { groupAdjustment = -size; + } } if (groupAdjustment != 0) @@ -1662,7 +1702,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } if (!appendHistoryItem) + { addHistoryItem(ssc); + } repaint(); } @@ -1997,7 +2039,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { AlignmentAnnotation sann[] = sequences[i].getAnnotation(); if (sann == null) + { continue; + } for (int avnum = 0; avnum < alview.length; avnum++) { if (alview[avnum] != alignment) @@ -4643,7 +4687,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, if (ds.getSequences() == null || !ds.getSequences().contains( sprods[s].getDatasetSequence())) + { ds.addSequence(sprods[s].getDatasetSequence()); + } sprods[s].updatePDBIds(); } Alignment al = new Alignment(sprods); diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java index 105209f..a19e1db 100644 --- a/src/jalview/gui/Jalview2XML.java +++ b/src/jalview/gui/Jalview2XML.java @@ -20,26 +20,51 @@ */ 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; @@ -51,6 +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. * @@ -678,7 +738,9 @@ public class Jalview2XML .startsWith( jmol.jmb.pdbentry[peid].getId() .toLowerCase()))) + { continue; + } if (matchedFile == null) { matchedFile = jmol.jmb.pdbentry[peid].getFile(); @@ -1371,18 +1433,26 @@ 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) @@ -2046,7 +2116,7 @@ public class Jalview2XML errorMessage = null; } - Hashtable alreadyLoadedPDB; + Hashtable alreadyLoadedPDB; /** * when set, local views will be updated from view stored in JalviewXML @@ -2058,10 +2128,14 @@ 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 { @@ -2409,7 +2483,9 @@ 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); @@ -2428,7 +2504,9 @@ public class Jalview2XML anpos = ae[aa].getPosition(); if (anpos >= anot.length) + { continue; + } anot[anpos] = new jalview.datamodel.Annotation( @@ -2522,10 +2600,14 @@ 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()) { @@ -2547,7 +2629,6 @@ public class Jalview2XML jaa.belowAlignment = an[i].isBelowAlignment(); } jaa.setCalcId(an[i].getCalcId()); - if (jaa.autoCalculated) { autoAlan.add(new JvAnnotRow(i, jaa)); @@ -3544,12 +3625,16 @@ 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( @@ -4392,7 +4477,9 @@ public class Jalview2XML } } else + { Cache.log.debug("Ignoring " + jvobj.getClass() + " (ID = " + id); + } } } diff --git a/src/jalview/gui/Jalview2XML_V1.java b/src/jalview/gui/Jalview2XML_V1.java index 946181c..b426914 100755 --- a/src/jalview/gui/Jalview2XML_V1.java +++ b/src/jalview/gui/Jalview2XML_V1.java @@ -20,18 +20,37 @@ */ package jalview.gui; -import java.io.*; -import java.util.*; -import java.util.jar.*; - -import javax.swing.*; - -import org.exolab.castor.xml.*; -import jalview.binding.*; -import jalview.schemes.*; +import jalview.binding.Annotation; +import jalview.binding.AnnotationElement; +import jalview.binding.Features; +import jalview.binding.JGroup; +import jalview.binding.JSeq; +import jalview.binding.JalviewModel; +import jalview.binding.JalviewModelSequence; +import jalview.binding.Pdbids; +import jalview.binding.Sequence; +import jalview.binding.SequenceSet; +import jalview.binding.Setting; +import jalview.binding.Tree; +import jalview.binding.UserColours; +import jalview.binding.Viewport; +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 java.io.InputStreamReader; +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! * @@ -120,7 +139,7 @@ public class Jalview2XML_V1 InputStreamReader in = new InputStreamReader(jin, "UTF-8"); JalviewModel object = new JalviewModel(); - object = (JalviewModel) object.unmarshal(in); + object = object.unmarshal(in); af = LoadFromObject(object, file); entryCount++; @@ -315,7 +334,7 @@ public class Jalview2XML_V1 for (int s = 0; s < ids.length; s++) { - seqs.addElement((jalview.datamodel.SequenceI) seqids + seqs.addElement(seqids .elementAt(ids[s])); } diff --git a/src/jalview/io/FileLoader.java b/src/jalview/io/FileLoader.java index 0f94efa..1d9655b 100755 --- a/src/jalview/io/FileLoader.java +++ b/src/jalview/io/FileLoader.java @@ -319,7 +319,6 @@ public class FileLoader implements Runnable } viewport.firePropertyChange("alignment", null, viewport .getAlignment().getSequences()); - } else { @@ -331,7 +330,9 @@ public class FileLoader implements Runnable { title })); if (!protocol.equals(AppletFormatAdapter.PASTE)) + { alignFrame.setFileName(file, format); + } if (raiseGUI) { // add the window to the GUI diff --git a/src/jalview/structure/StructureSelectionManager.java b/src/jalview/structure/StructureSelectionManager.java index 4d94b2d..58bba48 100644 --- a/src/jalview/structure/StructureSelectionManager.java +++ b/src/jalview/structure/StructureSelectionManager.java @@ -253,7 +253,7 @@ public class StructureSelectionManager boolean first = true; for (int i = 0; i < pdb.chains.size(); i++) { - PDBChain chain = ((PDBChain) pdb.chains.elementAt(i)); + PDBChain chain = (pdb.chains.elementAt(i)); if (targetChain.length() > 0 && !targetChain.equals(chain.id) && !infChain) { @@ -262,8 +262,8 @@ public class StructureSelectionManager // TODO: correctly determine sequence type for mixed na/peptide // structures AlignSeq as = new AlignSeq(sequence[s], - ((PDBChain) pdb.chains.elementAt(i)).sequence, - ((PDBChain) pdb.chains.elementAt(i)).isNa ? AlignSeq.DNA + pdb.chains.elementAt(i).sequence, + pdb.chains.elementAt(i).isNa ? AlignSeq.DNA : AlignSeq.PEP); as.calcScoreMatrix(); as.traceAlignment(); -- 1.7.10.2