mmCIF File Format

General
-
+
reinstate CTRL-click for opening pop-up menu on OSX

Application

@@ -1392,10 +1392,7 @@ between different screens.
New preference items for sequence ID tooltip and consensus annotation
-
Client to submit sequences and IDs to Envision2 - Workflows -
+
Client to submit sequences and IDs to Envision2 Workflows

Vamsas Capabilities

Improved VAMSAS synchronization (Jalview archive diff --git a/help/html/webServices/AACon.html b/help/html/webServices/AACon.html index 5dd4472..6d4a461 100644 --- a/help/html/webServices/AACon.html +++ b/help/html/webServices/AACon.html @@ -32,7 +32,7 @@ Function, and Genetics 43(2): 227-241. PubMed or available on the Valdar Group publications page), but the SMERFs score was developed later and described by Manning et al. in 2008 (REST web services exposing sequence alignment, analysis, and secondary structure prediction programs. Originally, Jalview 2's services were maintained by the Barton group at the University of - Dundee, and ran programs on the Life Sciences High-performace + Dundee, and ran programs on the Life Sciences High-performance Computing Cluster. With the advent of JABAWS, however, it is possible for anyone to host Jalview web diff --git a/help/html/webServices/urllinks.html b/help/html/webServices/urllinks.html index de0f8cd..7a23d58 100644 --- a/help/html/webServices/urllinks.html +++ b/help/html/webServices/urllinks.html @@ -83,7 +83,7 @@ Please Note:

The regular expressions supported by Jalview are those - provided by the Stevesoft + provided by the Stevesoft javaregex package.

Some characters must be escaped when specifying them as diff --git a/resources/lang/Messages_es.properties b/resources/lang/Messages_es.properties index 8943860..b3da568 100644 --- a/resources/lang/Messages_es.properties +++ b/resources/lang/Messages_es.properties @@ -321,7 +321,7 @@ action.save_vamsas_session = Guardar Sesi label.select_vamsas_session_opened_as_new_vamsas_session= Selecciones una sesión vamsas para abrirla como una nueva sesión. label.open_saved_vamsas_session = Abrir una sesión VAMSAS guardada label.groovy_console = Consola Groovy -label.lineart = lineart +label.lineart = Lineart label.dont_ask_me_again = No volver a preguntar label.select_eps_character_rendering_style = Seleccionar el carácter EPS como estilo de visualización label.invert_selection = Invertir selección diff --git a/src/ext/edu/ucsf/rbvi/strucviz2/ChimeraManager.java b/src/ext/edu/ucsf/rbvi/strucviz2/ChimeraManager.java index 4201f43..c0c7c46 100644 --- a/src/ext/edu/ucsf/rbvi/strucviz2/ChimeraManager.java +++ b/src/ext/edu/ucsf/rbvi/strucviz2/ChimeraManager.java @@ -199,8 +199,9 @@ public class ChimeraManager return null; } - List newModelList = getModelList(); - for (ChimeraModel newModel : newModelList) + // patch for Jalview - set model name in Chimera + // TODO: find a variant that works for sub-models + for (ChimeraModel newModel : getModelList()) { if (!modelList.contains(newModel)) { @@ -209,15 +210,12 @@ public class ChimeraManager "setattr M name " + modelName + " #" + newModel.getModelNumber(), false); modelList.add(newModel); - } } // assign color and residues to open models for (ChimeraModel chimeraModel : modelList) { - // // patch for Jalview - set model name in Chimera - // // TODO: find a variant that works for sub-models // get model color Color modelColor = getModelColor(chimeraModel); if (modelColor != null) @@ -731,7 +729,7 @@ public class ChimeraManager */ public List sendChimeraCommand(String command, boolean reply) { - // System.out.println("chimeradebug>> " + command); + // System.out.println("chimeradebug>> " + command); if (!isChimeraLaunched() || command == null || "".equals(command.trim())) { diff --git a/src/jalview/analysis/Conservation.java b/src/jalview/analysis/Conservation.java index d4ae57d..7b3ce25 100755 --- a/src/jalview/analysis/Conservation.java +++ b/src/jalview/analysis/Conservation.java @@ -235,10 +235,7 @@ public class Conservation c = '-'; } - if (!canonicaliseAa && 'a' <= c && c <= 'z') - { - c -= (32); // 32 = 'a' - 'A' - } + c = toUpperCase(c); } values[c]++; } @@ -326,6 +323,7 @@ public class Conservation } else { + c = toUpperCase(c); nres++; if (nres == 1) @@ -347,6 +345,22 @@ public class Conservation } /** + * Returns the upper-cased character if between 'a' and 'z', else the + * unchanged value + * + * @param c + * @return + */ + char toUpperCase(char c) + { + if ('a' <= c && c <= 'z') + { + c -= (32); // 32 = 'a' - 'A' + } + return c; + } + + /** * Calculates the conservation sequence * * @param consflag diff --git a/src/jalview/analysis/SequenceIdMatcher.java b/src/jalview/analysis/SequenceIdMatcher.java index 70defb0..f744ed1 100755 --- a/src/jalview/analysis/SequenceIdMatcher.java +++ b/src/jalview/analysis/SequenceIdMatcher.java @@ -290,7 +290,7 @@ public class SequenceIdMatcher { if (s != null) { - id = new String(s); + id = new String(s.toLowerCase()); } else { diff --git a/src/jalview/api/DBRefEntryI.java b/src/jalview/api/DBRefEntryI.java index 9415745..490b21a 100644 --- a/src/jalview/api/DBRefEntryI.java +++ b/src/jalview/api/DBRefEntryI.java @@ -2,6 +2,7 @@ package jalview.api; import jalview.datamodel.Mapping; +//JBPComment: this is a datamodel API - so it should be in datamodel (it's a peer of SequenceI) public interface DBRefEntryI { diff --git a/src/jalview/api/SiftsClientI.java b/src/jalview/api/SiftsClientI.java index e2fac14..527ae17 100644 --- a/src/jalview/api/SiftsClientI.java +++ b/src/jalview/api/SiftsClientI.java @@ -29,6 +29,8 @@ import jalview.xml.binding.sifts.Entry.Entity; import java.util.HashMap; import java.util.HashSet; +// JBPComment: this isn't a top-level Jalview API - should be in its own package api + public interface SiftsClientI { /** diff --git a/src/jalview/appletgui/AnnotationLabels.java b/src/jalview/appletgui/AnnotationLabels.java index 5727e9c..b28ccc7 100755 --- a/src/jalview/appletgui/AnnotationLabels.java +++ b/src/jalview/appletgui/AnnotationLabels.java @@ -162,6 +162,7 @@ public class AnnotationLabels extends Panel implements ActionListener, return row; } + @Override public void actionPerformed(ActionEvent evt) { AlignmentAnnotation[] aa = av.getAlignment().getAlignmentAnnotation(); @@ -261,6 +262,7 @@ public class AnnotationLabels extends Panel implements ActionListener, boolean resizePanel = false; + @Override public void mouseMoved(MouseEvent evt) { resizePanel = evt.getY() < 10 && evt.getX() < 14; @@ -306,6 +308,7 @@ public class AnnotationLabels extends Panel implements ActionListener, dragCancelled = true; } + @Override public void mouseDragged(MouseEvent evt) { if (dragCancelled) @@ -365,10 +368,12 @@ public class AnnotationLabels extends Panel implements ActionListener, } } + @Override public void mouseClicked(MouseEvent evt) { } + @Override public void mouseReleased(MouseEvent evt) { if (!resizePanel && !dragCancelled) @@ -400,6 +405,7 @@ public class AnnotationLabels extends Panel implements ActionListener, ap.annotationPanel.repaint(); } + @Override public void mouseEntered(MouseEvent evt) { if (evt.getY() < 10 && evt.getX() < 14) @@ -409,6 +415,7 @@ public class AnnotationLabels extends Panel implements ActionListener, } } + @Override public void mouseExited(MouseEvent evt) { dragCancelled = false; @@ -427,6 +434,7 @@ public class AnnotationLabels extends Panel implements ActionListener, repaint(); } + @Override public void mousePressed(MouseEvent evt) { oldY = evt.getY(); @@ -522,6 +530,7 @@ public class AnnotationLabels extends Panel implements ActionListener, final AlignmentAnnotation aaa = aa[selectedRow]; cbmi.addItemListener(new ItemListener() { + @Override public void itemStateChanged(ItemEvent e) { if (aaa.groupRef != null) @@ -545,6 +554,7 @@ public class AnnotationLabels extends Panel implements ActionListener, aa[selectedRow].groupRef.isShowConsensusHistogram()); chist.addItemListener(new ItemListener() { + @Override public void itemStateChanged(ItemEvent e) { // TODO: pass on reference @@ -564,6 +574,7 @@ public class AnnotationLabels extends Panel implements ActionListener, aa[selectedRow].groupRef.isShowSequenceLogo()); cprofl.addItemListener(new ItemListener() { + @Override public void itemStateChanged(ItemEvent e) { // TODO: pass on reference @@ -585,6 +596,7 @@ public class AnnotationLabels extends Panel implements ActionListener, aa[selectedRow].groupRef.isNormaliseSequenceLogo()); cprofn.addItemListener(new ItemListener() { + @Override public void itemStateChanged(ItemEvent e) { // TODO: pass on reference @@ -608,6 +620,7 @@ public class AnnotationLabels extends Panel implements ActionListener, av.isShowConsensusHistogram()); chist.addItemListener(new ItemListener() { + @Override public void itemStateChanged(ItemEvent e) { // TODO: pass on reference @@ -631,6 +644,7 @@ public class AnnotationLabels extends Panel implements ActionListener, av.isShowSequenceLogo()); cprof.addItemListener(new ItemListener() { + @Override public void itemStateChanged(ItemEvent e) { // TODO: pass on reference @@ -655,6 +669,7 @@ public class AnnotationLabels extends Panel implements ActionListener, av.isNormaliseSequenceLogo()); cprofn.addItemListener(new ItemListener() { + @Override public void itemStateChanged(ItemEvent e) { // TODO: pass on reference @@ -697,11 +712,47 @@ public class AnnotationLabels extends Panel implements ActionListener, // todo: make the ap scroll to the selection - not necessary, first // click highlights/scrolls, second selects ap.seqPanel.ap.idPanel.highlightSearchResults(null); - ap.av.setSelectionGroup(// new SequenceGroup( - aa[selectedRow].groupRef); // ); - ap.av.sendSelection(); + // process modifiers + SequenceGroup sg = ap.av.getSelectionGroup(); + if (sg == null + || sg == aa[selectedRow].groupRef + || !(jalview.util.Platform.isControlDown(evt) || evt + .isShiftDown())) + { + if (jalview.util.Platform.isControlDown(evt) + || evt.isShiftDown()) + { + // clone a new selection group from the associated group + ap.av.setSelectionGroup(new SequenceGroup( + aa[selectedRow].groupRef)); + } + else + { + // set selection to the associated group so it can be edited + ap.av.setSelectionGroup(aa[selectedRow].groupRef); + } + } + else + { + // modify current selection with associated group + int remainToAdd = aa[selectedRow].groupRef.getSize(); + for (SequenceI sgs : aa[selectedRow].groupRef.getSequences()) + { + if (jalview.util.Platform.isControlDown(evt)) + { + sg.addOrRemove(sgs, --remainToAdd == 0); + } + else + { + // notionally, we should also add intermediate sequences from + // last added sequence ? + sg.addSequence(sgs, --remainToAdd == 0); + } + } + } ap.paintAlignment(false); PaintRefresher.Refresh(ap, ap.av.getSequenceSetId()); + ap.av.sendSelection(); } else { @@ -728,7 +779,8 @@ public class AnnotationLabels extends Panel implements ActionListener, // we make a copy rather than edit the current selection if no // modifiers pressed // see Enhancement JAL-1557 - if (!(evt.isControlDown() || evt.isShiftDown())) + if (!(jalview.util.Platform.isControlDown(evt) || evt + .isShiftDown())) { sg = new SequenceGroup(sg); sg.clear(); @@ -736,7 +788,7 @@ public class AnnotationLabels extends Panel implements ActionListener, } else { - if (evt.isControlDown()) + if (jalview.util.Platform.isControlDown(evt)) { sg.addOrRemove(aa[selectedRow].sequenceRef, true); } @@ -794,11 +846,13 @@ public class AnnotationLabels extends Panel implements ActionListener, } } + @Override public void update(Graphics g) { paint(g); } + @Override public void paint(Graphics g) { int w = getSize().width; diff --git a/src/jalview/appletgui/IdPanel.java b/src/jalview/appletgui/IdPanel.java index 8f24f11..36c2199 100755 --- a/src/jalview/appletgui/IdPanel.java +++ b/src/jalview/appletgui/IdPanel.java @@ -100,6 +100,7 @@ public class IdPanel extends Panel implements MouseListener, Tooltip tooltip; + @Override public void mouseMoved(MouseEvent e) { int seq = alignPanel.seqPanel.findSeq(e); @@ -188,6 +189,7 @@ public class IdPanel extends Panel implements MouseListener, tooltiptext = null; } + @Override public void mouseDragged(MouseEvent e) { mouseDragging = true; @@ -207,6 +209,7 @@ public class IdPanel extends Panel implements MouseListener, alignPanel.paintAlignment(false); } + @Override public void mouseClicked(MouseEvent e) { if (e.getClickCount() < 2) @@ -270,6 +273,7 @@ public class IdPanel extends Panel implements MouseListener, } } + @Override public void mouseEntered(MouseEvent e) { if (scrollThread != null) @@ -278,6 +282,7 @@ public class IdPanel extends Panel implements MouseListener, } } + @Override public void mouseExited(MouseEvent e) { if (av.getWrapAlignment()) @@ -297,6 +302,7 @@ public class IdPanel extends Panel implements MouseListener, } } + @Override public void mousePressed(MouseEvent e) { if (e.getClickCount() > 1) @@ -345,7 +351,8 @@ public class IdPanel extends Panel implements MouseListener, } if ((av.getSelectionGroup() == null) - || ((!e.isControlDown() && !e.isShiftDown()) && av + || ((!jalview.util.Platform.isControlDown(e) && !e + .isShiftDown()) && av .getSelectionGroup() != null)) { av.setSelectionGroup(new SequenceGroup()); @@ -401,6 +408,7 @@ public class IdPanel extends Panel implements MouseListener, } + @Override public void mouseReleased(MouseEvent e) { if (scrollThread != null) @@ -455,6 +463,7 @@ public class IdPanel extends Panel implements MouseListener, running = false; } + @Override public void run() { running = true; diff --git a/src/jalview/appletgui/SeqPanel.java b/src/jalview/appletgui/SeqPanel.java index 479b746..31bf6a4 100644 --- a/src/jalview/appletgui/SeqPanel.java +++ b/src/jalview/appletgui/SeqPanel.java @@ -1813,9 +1813,12 @@ public class SeqPanel extends Panel implements MouseMotionListener, // do we want to thread this ? (contention with seqsel and colsel locks, I // suspect) - // rules are: colsel is copied if there is a real intersection between - // sequence selection - boolean repaint = false, copycolsel = true; + /* + * only copy colsel if there is a real intersection between + * sequence selection and this panel's alignment + */ + boolean repaint = false; + boolean copycolsel = false; if (av.getSelectionGroup() == null || !av.isSelectionGroupChanged(true)) { SequenceGroup sgroup = null; @@ -1832,11 +1835,9 @@ public class SeqPanel extends Panel implements MouseMotionListener, } sgroup = seqsel.intersect(av.getAlignment(), (av.hasHiddenRows()) ? av.getHiddenRepSequences() : null); - if ((sgroup == null || sgroup.getSize() == 0) - && (colsel == null || colsel.isEmpty())) + if ((sgroup != null && sgroup.getSize() > 0)) { - // don't copy columns if the region didn't intersect. - copycolsel = false; + copycolsel = true; } } if (sgroup != null && sgroup.getSize() > 0) @@ -1964,7 +1965,6 @@ public class SeqPanel extends Panel implements MouseMotionListener, ColumnSelection cs = MappingUtils.mapColumnSelection(colsel, sourceAv, av); av.setColumnSelection(cs); - av.isColSelChanged(true); ap.scalePanelHolder.repaint(); ap.repaint(); diff --git a/src/jalview/bin/Cache.java b/src/jalview/bin/Cache.java index 7911cd5..38aa55f 100755 --- a/src/jalview/bin/Cache.java +++ b/src/jalview/bin/Cache.java @@ -426,7 +426,7 @@ public class Cache System.out .println("Jalview Version: " + codeVersion + codeInstallation); - Pdb.setCurrentDefaultFomart(jalview.bin.Cache.getDefault( + Pdb.setCurrentDefaultFormat(jalview.bin.Cache.getDefault( "DEFAULT_STRUCTURE_FORMAT", DEFAULT_STRUCTURE_FORMAT)); // jnlpVersion will be null if we're using InstallAnywhere // Dont do this check if running in headless mode diff --git a/src/jalview/datamodel/ColumnSelection.java b/src/jalview/datamodel/ColumnSelection.java index 6fd76b2..aaf70b8 100644 --- a/src/jalview/datamodel/ColumnSelection.java +++ b/src/jalview/datamodel/ColumnSelection.java @@ -32,10 +32,14 @@ import java.util.List; import java.util.Vector; /** - * NOTE: Columns are zero based. + * Data class holding the selected columns and hidden column ranges for a view. + * Ranges are base 1. */ public class ColumnSelection { + /** + * A class to hold an efficient representation of selected columns + */ private class IntList { /* @@ -205,9 +209,26 @@ public class ColumnSelection } return rlist; } + + @Override + public int hashCode() + { + // TODO Auto-generated method stub + return selected.hashCode(); + } + + @Override + public boolean equals(Object obj) + { + if (obj instanceof IntList) + { + return ((IntList) obj).selected.equals(selected); + } + return false; + } } - IntList selected = new IntList(); + IntList selection = new IntList(); /* * list of hidden column [start, end] ranges; the list is maintained in @@ -223,7 +244,7 @@ public class ColumnSelection */ public void addElement(int col) { - selected.add(col); + selection.add(col); } /** @@ -231,7 +252,7 @@ public class ColumnSelection */ public void clear() { - selected.clear(); + selection.clear(); } /** @@ -242,7 +263,7 @@ public class ColumnSelection */ public void removeElement(int col) { - selected.remove(col); + selection.remove(col); } /** @@ -259,9 +280,9 @@ public class ColumnSelection for (int i = start; i < end; i++) { colInt = new Integer(i); - if (selected.contains(colInt)) + if (selection.contains(colInt)) { - selected.remove(colInt); + selection.remove(colInt); } } } @@ -273,7 +294,7 @@ public class ColumnSelection */ public List getSelected() { - return selected.getList(); + return selection.getList(); } /** @@ -282,7 +303,7 @@ public class ColumnSelection */ public List getSelectedRanges() { - return selected.getRanges(); + return selection.getRanges(); } /** @@ -294,7 +315,7 @@ public class ColumnSelection */ public boolean contains(int col) { - return (col > -1) ? selected.isSelected(col) : false; + return (col > -1) ? selection.isSelected(col) : false; } /** @@ -302,7 +323,7 @@ public class ColumnSelection */ public boolean isEmpty() { - return selected == null || selected.isEmpty(); + return selection == null || selection.isEmpty(); } /** @@ -312,11 +333,11 @@ public class ColumnSelection */ public int getMax() { - if (selected.isEmpty()) + if (selection.isEmpty()) { return -1; } - return selected.getMaxColumn(); + return selection.getMaxColumn(); } /** @@ -326,11 +347,11 @@ public class ColumnSelection */ public int getMin() { - if (selected.isEmpty()) + if (selection.isEmpty()) { return 1000000000; } - return selected.getMinColumn(); + return selection.getMinColumn(); } /** @@ -344,7 +365,7 @@ public class ColumnSelection public List compensateForEdit(int start, int change) { List deletedHiddenColumns = null; - selected.compensateForEdits(start, change); + selection.compensateForEdits(start, change); if (hiddenColumns != null) { @@ -394,7 +415,7 @@ public class ColumnSelection private void compensateForDelEdits(int start, int change) { - selected.compensateForEdits(start, change); + selection.compensateForEdits(start, change); if (hiddenColumns != null) { @@ -571,12 +592,12 @@ public class ColumnSelection hiddenColumns = null; } } - if (selected != null && selected.size() > 0) + if (selection != null && selection.size() > 0) { - selected.pruneColumnList(shifts); - if (selected != null && selected.size() == 0) + selection.pruneColumnList(shifts); + if (selection != null && selection.size() == 0) { - selected = null; + selection = null; } } // and shift the rest. @@ -743,13 +764,13 @@ public class ColumnSelection public void hideSelectedColumns() { - synchronized (selected) + synchronized (selection) { - for (int[] selregions : selected.getRanges()) + for (int[] selregions : selection.getRanges()) { hideColumns(selregions[0], selregions[1]); } - selected.clear(); + selection.clear(); } } @@ -927,12 +948,12 @@ public class ColumnSelection { if (copy != null) { - if (copy.selected != null) + if (copy.selection != null) { - selected = new IntList(); - for (int i = 0, j = copy.selected.size(); i < j; i++) + selection = new IntList(); + for (int i = 0, j = copy.selection.size(); i < j; i++) { - selected.add(copy.selected.elementAt(i)); + selection.add(copy.selection.elementAt(i)); } } if (copy.hiddenColumns != null) @@ -1307,7 +1328,7 @@ public class ColumnSelection { if (hiddenColumns != null && isVisible(col.intValue())) { - selected.add(col); + selection.add(col); } } } @@ -1321,8 +1342,8 @@ public class ColumnSelection */ public void setElementsFrom(ColumnSelection colsel) { - selected = new IntList(); - if (colsel.selected != null && colsel.selected.size() > 0) + selection = new IntList(); + if (colsel.selection != null && colsel.selection.size() > 0) { if (hiddenColumns != null && hiddenColumns.size() > 0) { @@ -1489,7 +1510,7 @@ public class ColumnSelection */ public boolean hasSelectedColumns() { - return (selected != null && selected.size() > 0); + return (selection != null && selection.size() > 0); } /** @@ -1612,4 +1633,74 @@ public class ColumnSelection return false; } + /** + * Returns a hashCode built from selected columns and hidden column ranges + */ + @Override + public int hashCode() + { + int hashCode = selection.hashCode(); + if (hiddenColumns != null) + { + for (int[] hidden : hiddenColumns) + { + hashCode = 31 * hashCode + hidden[0]; + hashCode = 31 * hashCode + hidden[1]; + } + } + return hashCode; + } + + /** + * Answers true if comparing to a ColumnSelection with the same selected + * columns and hidden columns, else false + */ + @Override + public boolean equals(Object obj) + { + if (!(obj instanceof ColumnSelection)) + { + return false; + } + ColumnSelection that = (ColumnSelection) obj; + + /* + * check columns selected are either both null, or match + */ + if (this.selection == null) + { + if (that.selection != null) + { + return false; + } + } + if (!this.selection.equals(that.selection)) + { + return false; + } + + /* + * check hidden columns are either both null, or match + */ + if (this.hiddenColumns == null) + { + return (that.hiddenColumns == null); + } + if (that.hiddenColumns == null + || that.hiddenColumns.size() != this.hiddenColumns.size()) + { + return false; + } + int i = 0; + for (int[] thisRange : hiddenColumns) + { + int[] thatRange = that.hiddenColumns.get(i++); + if (thisRange[0] != thatRange[0] || thisRange[1] != thatRange[1]) + { + return false; + } + } + return true; + } + } diff --git a/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java b/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java index 1ce0d2b..944ef52 100644 --- a/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java +++ b/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java @@ -101,17 +101,13 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel private String lastCommand; - private boolean loadedInline; - - /** + /* * current set of model filenames loaded */ String[] modelFileNames = null; String lastHighlightCommand; - private List lastReply; - /* * incremented every time a load notification is successfully handled - * lightweight mechanism for other threads to detect when they can start @@ -617,7 +613,8 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel if (lastCommand == null || !lastCommand.equals(command)) { // trim command or it may never find a match in the replyLog!! - lastReply = viewer.sendChimeraCommand(command.trim(), logResponse); + List lastReply = viewer.sendChimeraCommand(command.trim(), + logResponse); if (logResponse && debug) { log("Response from command ('" + command + "') was:\n" + lastReply); @@ -715,17 +712,6 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel // End StructureListener // ////////////////////////// - public Color getColour(int atomIndex, int pdbResNum, String chain, - String pdbfile) - { - if (getModelNum(pdbfile) < 0) - { - return null; - } - log("get model / residue colour attribute unimplemented"); - return null; - } - /** * returns the current featureRenderer that should be used to colour the * structures @@ -795,15 +781,6 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel } /** - * map from string to applet - */ - public Map getRegistryInfo() - { - // TODO Auto-generated method stub - return null; - } - - /** * returns the current sequenceRenderer that should be used to colour the * structures * @@ -815,20 +792,18 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel AlignmentViewPanel alignment); /** - * Construct and send a command to highlight zero, one or more atoms. - * - *
- * Done by generating a command like (to 'highlight' positions 44 and 46) - * show #0:44,46.C - *
+ * Construct and send a command to highlight zero, one or more atoms. We do + * this by sending an "rlabel" command to show the residue label at that + * position. */ @Override public void highlightAtoms(List atoms) { - if (atoms == null) + if (atoms == null || atoms.size() == 0) { return; } + StringBuilder cmd = new StringBuilder(128); boolean first = true; boolean found = false; @@ -843,7 +818,7 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel { if (first) { - cmd.append("show #").append(cms.get(0).getModelNumber()) + cmd.append("rlabel #").append(cms.get(0).getModelNumber()) .append(":"); } else @@ -851,7 +826,6 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel cmd.append(","); } first = false; - cmd.append(cms.get(0).getModelNumber()).append(":"); cmd.append(pdbResNum); if (!chain.equals(" ")) { @@ -863,19 +837,24 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel String command = cmd.toString(); /* - * Avoid repeated commands for the same residue + * avoid repeated commands for the same residue */ if (command.equals(lastHighlightCommand)) { return; } - viewerCommandHistory(false); + /* + * unshow the label for the previous residue + */ + if (lastHighlightCommand != null) + { + viewer.sendChimeraCommand("~" + lastHighlightCommand, false); + } if (found) { - viewer.sendChimeraCommand(command.toString(), false); + viewer.sendChimeraCommand(command, false); } - viewerCommandHistory(true); this.lastHighlightCommand = command; } diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java index 7e7bdd3..d9d5f27 100644 --- a/src/jalview/gui/AlignFrame.java +++ b/src/jalview/gui/AlignFrame.java @@ -113,7 +113,6 @@ import java.awt.datatransfer.Clipboard; import java.awt.datatransfer.DataFlavor; import java.awt.datatransfer.StringSelection; import java.awt.datatransfer.Transferable; -import java.awt.dnd.DnDConstants; import java.awt.dnd.DropTargetDragEvent; import java.awt.dnd.DropTargetDropEvent; import java.awt.dnd.DropTargetEvent; @@ -1327,15 +1326,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, alignmentToExport = viewport.getAlignment(); alignmentStartEnd = viewport.getAlignment() .getVisibleStartAndEndIndex( - viewport - .getColumnSelection().getHiddenColumns()); + viewport.getColumnSelection().getHiddenColumns()); } AlignmentExportData ed = new AlignmentExportData(alignmentToExport, omitHidden, alignmentStartEnd, settings); return ed; } - /** * DOCUMENT ME! * @@ -4845,15 +4842,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } } catch (Exception e) { - Cache.log.error( - "Exception when finding crossreferences", e); + Cache.log.error("Exception when finding crossreferences", e); } catch (OutOfMemoryError e) { new OOMWarning("whilst fetching crossreferences", e); } catch (Throwable e) { - Cache.log.error("Error when finding crossreferences", - e); + Cache.log.error("Error when finding crossreferences", e); } finally { AlignFrame.this.setProgressBar(MessageManager.formatMessage( @@ -5030,49 +5025,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, public void drop(DropTargetDropEvent evt) { Transferable t = evt.getTransferable(); - java.util.List files = null; + java.util.List files = new ArrayList(), protocols = new ArrayList(); try { - DataFlavor uriListFlavor = new DataFlavor( - "text/uri-list;class=java.lang.String"); - if (t.isDataFlavorSupported(DataFlavor.javaFileListFlavor)) - { - // Works on Windows and MacOSX - evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE); - files = (java.util.List) t - .getTransferData(DataFlavor.javaFileListFlavor); - } - else if (t.isDataFlavorSupported(uriListFlavor)) - { - // This is used by Unix drag system - evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE); - String data = (String) t.getTransferData(uriListFlavor); - files = new java.util.ArrayList(1); - for (java.util.StringTokenizer st = new java.util.StringTokenizer( - data, "\r\n"); st.hasMoreTokens();) - { - String s = st.nextToken(); - if (s.startsWith("#")) - { - // the line is a comment (as per the RFC 2483) - continue; - } - - java.net.URI uri = new java.net.URI(s); - // check to see if we can handle this kind of URI - if (uri.getScheme().toLowerCase().startsWith("http")) - { - files.add(uri.toString()); - } - else - { - // otherwise preserve old behaviour: catch all for file objects - java.io.File file = new java.io.File(uri); - files.add(file.toString()); - } - } - } + Desktop.transferFromDropTarget(files, protocols, evt, t); } catch (Exception e) { e.printStackTrace(); @@ -5547,8 +5504,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, AlignFrame.this.setMenusForViewport(); } }); - dbRefFetcher - .fetchDBRefs(false); + dbRefFetcher.fetchDBRefs(false); } }).start(); @@ -6106,9 +6062,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, try { Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true)); - al = dna.reverseCdna(complement); viewport.addAlignment(al, ""); + addHistoryItem(new EditCommand( + MessageManager.getString("label.add_sequences"), + Action.PASTE, al.getSequencesArray(), 0, al.getWidth(), + viewport.getAlignment())); } catch (Exception ex) { System.err.println(ex.getMessage()); diff --git a/src/jalview/gui/AnnotationLabels.java b/src/jalview/gui/AnnotationLabels.java index 68df498..e27b919 100755 --- a/src/jalview/gui/AnnotationLabels.java +++ b/src/jalview/gui/AnnotationLabels.java @@ -802,8 +802,45 @@ public class AnnotationLabels extends JPanel implements MouseListener, // todo: make the ap scroll to the selection - not necessary, first // click highlights/scrolls, second selects ap.getSeqPanel().ap.getIdPanel().highlightSearchResults(null); - ap.av.setSelectionGroup(// new SequenceGroup( - aa[selectedRow].groupRef); // ); + // process modifiers + SequenceGroup sg = ap.av.getSelectionGroup(); + if (sg == null + || sg == aa[selectedRow].groupRef + || !(jalview.util.Platform.isControlDown(evt) || evt + .isShiftDown())) + { + if (jalview.util.Platform.isControlDown(evt) + || evt.isShiftDown()) + { + // clone a new selection group from the associated group + ap.av.setSelectionGroup(new SequenceGroup( + aa[selectedRow].groupRef)); + } + else + { + // set selection to the associated group so it can be edited + ap.av.setSelectionGroup(aa[selectedRow].groupRef); + } + } + else + { + // modify current selection with associated group + int remainToAdd = aa[selectedRow].groupRef.getSize(); + for (SequenceI sgs : aa[selectedRow].groupRef.getSequences()) + { + if (jalview.util.Platform.isControlDown(evt)) + { + sg.addOrRemove(sgs, --remainToAdd == 0); + } + else + { + // notionally, we should also add intermediate sequences from + // last added sequence ? + sg.addSequence(sgs, --remainToAdd == 0); + } + } + } + ap.paintAlignment(false); PaintRefresher.Refresh(ap, ap.av.getSequenceSetId()); ap.av.sendSelection(); @@ -833,7 +870,8 @@ public class AnnotationLabels extends JPanel implements MouseListener, // we make a copy rather than edit the current selection if no // modifiers pressed // see Enhancement JAL-1557 - if (!(evt.isControlDown() || evt.isShiftDown())) + if (!(jalview.util.Platform.isControlDown(evt) || evt + .isShiftDown())) { sg = new SequenceGroup(sg); sg.clear(); @@ -841,7 +879,7 @@ public class AnnotationLabels extends JPanel implements MouseListener, } else { - if (evt.isControlDown()) + if (jalview.util.Platform.isControlDown(evt)) { sg.addOrRemove(aa[selectedRow].sequenceRef, true); } @@ -861,9 +899,9 @@ public class AnnotationLabels extends JPanel implements MouseListener, sg.addSequence(aa[selectedRow].sequenceRef, false); } ap.av.setSelectionGroup(sg); - ap.av.sendSelection(); ap.paintAlignment(false); PaintRefresher.Refresh(ap, ap.av.getSequenceSetId()); + ap.av.sendSelection(); } } diff --git a/src/jalview/gui/Desktop.java b/src/jalview/gui/Desktop.java index 7f36f7f..698b164 100644 --- a/src/jalview/gui/Desktop.java +++ b/src/jalview/gui/Desktop.java @@ -952,53 +952,15 @@ public class Desktop extends jalview.jbgui.GDesktop implements { boolean success = true; Transferable t = evt.getTransferable(); - java.util.List files = null; - java.util.List protocols = null; + java.util.List files = new ArrayList(); + java.util.List protocols = new ArrayList(); try { - DataFlavor uriListFlavor = new DataFlavor( - "text/uri-list;class=java.lang.String"); - if (t.isDataFlavorSupported(DataFlavor.javaFileListFlavor)) - { - // Works on Windows and MacOSX - evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE); - files = (java.util.List) t - .getTransferData(DataFlavor.javaFileListFlavor); - } - else if (t.isDataFlavorSupported(uriListFlavor)) - { - // This is used by Unix drag system - evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE); - String data = (String) t.getTransferData(uriListFlavor); - files = new java.util.ArrayList(1); - protocols = new java.util.ArrayList(1); - for (java.util.StringTokenizer st = new java.util.StringTokenizer( - data, "\r\n"); st.hasMoreTokens();) - { - String s = st.nextToken(); - if (s.startsWith("#")) - { - // the line is a comment (as per the RFC 2483) - continue; - } - java.net.URI uri = new java.net.URI(s); - if (uri.getScheme().toLowerCase().startsWith("http")) - { - protocols.add(FormatAdapter.URL); - files.add(uri.toString()); - } - else - { - // otherwise preserve old behaviour: catch all for file objects - java.io.File file = new java.io.File(uri); - protocols.add(FormatAdapter.FILE); - files.add(file.toString()); - } - } - } + Desktop.transferFromDropTarget(files, protocols, evt, t); } catch (Exception e) { + e.printStackTrace(); success = false; } @@ -3190,4 +3152,102 @@ public class Desktop extends jalview.jbgui.GDesktop implements return groovyConsole; } + public static void transferFromDropTarget(List files, + List protocols, DropTargetDropEvent evt, Transferable t) + throws Exception + { + + DataFlavor uriListFlavor = new DataFlavor( + "text/uri-list;class=java.lang.String"); + if (t.isDataFlavorSupported(DataFlavor.javaFileListFlavor)) + { + // Works on Windows and MacOSX + Cache.log.debug("Drop handled as javaFileListFlavor"); + evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE); + for (Object file : (List) t + .getTransferData(DataFlavor.javaFileListFlavor)) + { + files.add(((File)file).toString()); + protocols.add(FormatAdapter.FILE); + } + } + else + { + // Unix like behaviour + boolean added = false; + String data = null; + if (t.isDataFlavorSupported(uriListFlavor)) + { + Cache.log.debug("Drop handled as uriListFlavor"); + // This is used by Unix drag system + evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE); + data = (String) t.getTransferData(uriListFlavor); + } + if (data == null) + { + // fallback to text: workaround - on OSX where there's a JVM bug + Cache.log.debug("standard URIListFlavor failed. Trying text"); + // try text fallback + data = (String) t.getTransferData(new DataFlavor( + "text/plain;class=java.lang.String")); + if (Cache.log.isDebugEnabled()) + { + Cache.log.debug("fallback returned " + data); + } + } + while (protocols.size() < files.size()) + { + Cache.log.debug("Adding missing FILE protocol for " + + files.get(protocols.size())); + protocols.add(FormatAdapter.FILE); + } + for (java.util.StringTokenizer st = new java.util.StringTokenizer( + data, "\r\n"); st.hasMoreTokens();) + { + added = true; + String s = st.nextToken(); + if (s.startsWith("#")) + { + // the line is a comment (as per the RFC 2483) + continue; + } + java.net.URI uri = new java.net.URI(s); + if (uri.getScheme().toLowerCase().startsWith("http")) + { + protocols.add(FormatAdapter.URL); + files.add(uri.toString()); + } + else + { + // otherwise preserve old behaviour: catch all for file objects + java.io.File file = new java.io.File(uri); + protocols.add(FormatAdapter.FILE); + files.add(file.toString()); + } + } + if (Cache.log.isDebugEnabled()) + { + if (data == null || !added) + { + Cache.log + .debug("Couldn't resolve drop data. Here are the supported flavors:"); + for (DataFlavor fl : t.getTransferDataFlavors()) + { + Cache.log.debug("Supported transfer dataflavor: " + + fl.toString()); + evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE); + Object df = t.getTransferData(fl); + if (df != null) + { + Cache.log.debug("Retrieves: " + df); + } + else + { + Cache.log.debug("Retrieved nothing"); + } + } + } + } + } + } } diff --git a/src/jalview/gui/FeatureSettings.java b/src/jalview/gui/FeatureSettings.java index f250583..09204d1 100644 --- a/src/jalview/gui/FeatureSettings.java +++ b/src/jalview/gui/FeatureSettings.java @@ -1326,7 +1326,7 @@ public class FeatureSettings extends JPanel implements * * @return vector of selected das source nicknames */ - public Vector getSelectedSources() + public Vector getSelectedSources() { return dassourceBrowser.getSelectedSources(); } diff --git a/src/jalview/gui/IdPanel.java b/src/jalview/gui/IdPanel.java index c84505b..61ddafb 100755 --- a/src/jalview/gui/IdPanel.java +++ b/src/jalview/gui/IdPanel.java @@ -349,10 +349,9 @@ public class IdPanel extends JPanel implements MouseListener, return; } - if ((av.getSelectionGroup() == null) - || ((!e.isControlDown() && !e.isShiftDown()) && av - .getSelectionGroup() != null)) + || (!jalview.util.Platform.isControlDown(e) + && !e.isShiftDown() && av.getSelectionGroup() != null)) { av.setSelectionGroup(new SequenceGroup()); av.getSelectionGroup().setStartRes(0); diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java index 1e0772a..4b0ffad 100644 --- a/src/jalview/gui/PopupMenu.java +++ b/src/jalview/gui/PopupMenu.java @@ -60,6 +60,7 @@ import jalview.util.GroupUrlLink; import jalview.util.GroupUrlLink.UrlStringTooLongException; import jalview.util.MessageManager; import jalview.util.UrlLink; +import jalview.ws.DBRefFetcher; import java.awt.Color; import java.awt.event.ActionEvent; @@ -2389,11 +2390,11 @@ public class PopupMenu extends JPopupMenu @Override public void run() { - boolean isNuclueotide = ap.alignFrame.getViewport().getAlignment() + boolean isNucleotide = ap.alignFrame.getViewport().getAlignment() .isNucleotide(); - new jalview.ws.DBRefFetcher(sequences, ap.alignFrame, null, - ap.alignFrame.featureSettings, isNuclueotide) + new DBRefFetcher(sequences, ap.alignFrame, null, + ap.alignFrame.featureSettings, isNucleotide) .fetchDBRefs(false); } diff --git a/src/jalview/gui/Preferences.java b/src/jalview/gui/Preferences.java index 6b2d3c4..afc93e0 100755 --- a/src/jalview/gui/Preferences.java +++ b/src/jalview/gui/Preferences.java @@ -164,6 +164,16 @@ public class Preferences extends GPreferences private WsPreferences wsPrefs; + private OptionsParam promptEachTimeOpt = new OptionsParam( + MessageManager.getString("label.prompt_each_time"), + "Prompt each time"); + + private OptionsParam lineArtOpt = new OptionsParam( + MessageManager.getString("label.lineart"), "Lineart"); + + private OptionsParam textOpt = new OptionsParam( + MessageManager.getString("action.text"), "Text"); + /** * Creates a new Preferences object. */ @@ -359,12 +369,23 @@ public class Preferences extends GPreferences /* * Set Output tab defaults */ - epsRendering - .addItem(MessageManager.getString("label.prompt_each_time")); - epsRendering.addItem(MessageManager.getString("label.lineart")); - epsRendering.addItem(MessageManager.getString("action.text")); - epsRendering.setSelectedItem(Cache.getDefault("EPS_RENDERING", - "Prompt each time")); + epsRendering.addItem(promptEachTimeOpt); + epsRendering.addItem(lineArtOpt); + epsRendering.addItem(textOpt); + String defaultEPS = Cache.getDefault("EPS_RENDERING", + "Prompt each time"); + if (defaultEPS.equalsIgnoreCase("Text")) + { + epsRendering.setSelectedItem(textOpt); + } + else if (defaultEPS.equalsIgnoreCase("Lineart")) + { + epsRendering.setSelectedItem(lineArtOpt); + } + else + { + epsRendering.setSelectedItem(promptEachTimeOpt); + } autoIdWidth.setSelected(Cache.getDefault("FIGURE_AUTOIDWIDTH", false)); userIdWidth.setEnabled(!autoIdWidth.isSelected()); userIdWidthlabel.setEnabled(!autoIdWidth.isSelected()); @@ -515,15 +536,8 @@ public class Preferences extends GPreferences /* * Save Output settings */ - if (epsRendering.getSelectedItem().equals("Prompt each time")) - { - Cache.applicationProperties.remove("EPS_RENDERING"); - } - else - { - Cache.applicationProperties.setProperty("EPS_RENDERING", epsRendering - .getSelectedItem().toString()); - } + Cache.applicationProperties.setProperty("EPS_RENDERING", + ((OptionsParam) epsRendering.getSelectedItem()).getCode()); /* * Save Connections settings @@ -983,4 +997,57 @@ public class Preferences extends GPreferences } } + public class OptionsParam + { + private String name; + + private String code; + + public OptionsParam(String name, String code) + { + this.name = name; + this.code = code; + } + + public String getName() + { + return name; + } + + public void setName(String name) + { + this.name = name; + } + + public String getCode() + { + return code; + } + + public void setCode(String code) + { + this.code = code; + } + + @Override + public String toString() + { + return name; + } + + @Override + public boolean equals(Object that) + { + if (!(that instanceof OptionsParam)) + { + return false; + } + return this.code.equalsIgnoreCase(((OptionsParam) that).code); + } + + @Override + public int hashCode(){ + return name.hashCode() + code.hashCode(); + } + } } diff --git a/src/jalview/gui/ScalePanel.java b/src/jalview/gui/ScalePanel.java index f2cbf33..2165b2c 100755 --- a/src/jalview/gui/ScalePanel.java +++ b/src/jalview/gui/ScalePanel.java @@ -43,17 +43,14 @@ import javax.swing.JPopupMenu; import javax.swing.ToolTipManager; /** - * DOCUMENT ME! - * - * @author $author$ - * @version $Revision$ + * The panel containing the sequence ruler (when not in wrapped mode), and + * supports a range of mouse operations to select, hide or reveal columns. */ public class ScalePanel extends JPanel implements MouseMotionListener, MouseListener { protected int offy = 4; - /** DOCUMENT ME!! */ public int width; protected AlignViewport av; @@ -62,13 +59,26 @@ public class ScalePanel extends JPanel implements MouseMotionListener, boolean stretchingGroup = false; - int min; // used by mouseDragged to see if user + /* + * min, max hold the extent of a mouse drag action + */ + int min; - int max; // used by mouseDragged to see if user + int max; boolean mouseDragging = false; - // wants to delete columns + /* + * holds a hidden column range when the mouse is over an adjacent column + */ + int[] reveal; + + /** + * Constructor + * + * @param av + * @param ap + */ public ScalePanel(AlignViewport av, AlignmentPanel ap) { this.av = av; @@ -393,6 +403,8 @@ public class ScalePanel extends JPanel implements MouseMotionListener, @Override public void mouseMoved(MouseEvent evt) { + this.setToolTipText(null); + reveal = null; if (!av.hasHiddenColumns()) { return; @@ -402,7 +414,6 @@ public class ScalePanel extends JPanel implements MouseMotionListener, res = av.getColumnSelection().adjustForHiddenColumns(res); - reveal = null; if (av.getColumnSelection().getHiddenColumns() != null) { for (int[] region : av.getColumnSelection().getHiddenColumns()) @@ -415,17 +426,11 @@ public class ScalePanel extends JPanel implements MouseMotionListener, .getString("label.reveal_hidden_columns")); break; } - else - { - this.setToolTipText(null); - } } } repaint(); } - int[] reveal; - /** * DOCUMENT ME! * diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java index 3fbb809..2d44a0f 100644 --- a/src/jalview/gui/SeqPanel.java +++ b/src/jalview/gui/SeqPanel.java @@ -1947,10 +1947,12 @@ public class SeqPanel extends JPanel implements MouseListener, // do we want to thread this ? (contention with seqsel and colsel locks, I // suspect) - // rules are: colsel is copied if there is a real intersection between - // sequence selection + /* + * only copy colsel if there is a real intersection between + * sequence selection and this panel's alignment + */ boolean repaint = false; - boolean copycolsel = true; + boolean copycolsel = false; SequenceGroup sgroup = null; if (seqsel != null && seqsel.getSize() > 0) @@ -1964,11 +1966,9 @@ public class SeqPanel extends JPanel implements MouseListener, } sgroup = seqsel.intersect(av.getAlignment(), (av.hasHiddenRows()) ? av.getHiddenRepSequences() : null); - if ((sgroup == null || sgroup.getSize() == 0) - || (colsel == null || colsel.isEmpty())) + if ((sgroup != null && sgroup.getSize() > 0)) { - // don't copy columns if the region didn't intersect. - copycolsel = false; + copycolsel = true; } } if (sgroup != null && sgroup.getSize() > 0) @@ -2061,7 +2061,6 @@ public class SeqPanel extends JPanel implements MouseListener, ColumnSelection cs = MappingUtils.mapColumnSelection(colsel, sourceAv, av); av.setColumnSelection(cs); - av.isColSelChanged(true); PaintRefresher.Refresh(this, av.getSequenceSetId()); diff --git a/src/jalview/gui/SequenceFetcher.java b/src/jalview/gui/SequenceFetcher.java index e567d20..71c8a39 100755 --- a/src/jalview/gui/SequenceFetcher.java +++ b/src/jalview/gui/SequenceFetcher.java @@ -407,6 +407,10 @@ public class SequenceFetcher extends JPanel implements Runnable this.add(jPanel2, java.awt.BorderLayout.NORTH); jScrollPane1.getViewport().add(textArea); + /* + * open the database tree + */ + database.waitForInput(); } private void pdbSourceAction() diff --git a/src/jalview/gui/StructureChooser.java b/src/jalview/gui/StructureChooser.java index d924e73..46731e9 100644 --- a/src/jalview/gui/StructureChooser.java +++ b/src/jalview/gui/StructureChooser.java @@ -35,6 +35,7 @@ import jalview.fts.service.pdb.PDBFTSRestClient; import jalview.jbgui.GStructureChooser; import jalview.structure.StructureSelectionManager; import jalview.util.MessageManager; +import jalview.ws.DBRefFetcher; import jalview.ws.sifts.SiftsSettings; import java.awt.event.ItemEvent; @@ -800,6 +801,10 @@ public class StructureChooser extends GStructureChooser implements if (pdbEntry == null) { pdbEntry = new PDBEntry(); + if (pdbIdStr.split(":").length > 1) + { + pdbEntry.setChainCode(pdbIdStr.split(":")[1]); + } pdbEntry.setId(pdbIdStr); pdbEntry.setType(PDBEntry.Type.PDB); selectedSequence.getDatasetSequence().addPDBId(pdbEntry); @@ -860,31 +865,30 @@ public class StructureChooser extends GStructureChooser implements { ssm.setProgressBar(null); ssm.setProgressBar("Fetching Database refs.."); - new jalview.ws.DBRefFetcher(sequences, null, null, null, false) - .fetchDBRefs(true); + new DBRefFetcher(sequences).fetchDBRefs(true); break; } } } - if (pdbEntriesToView.length > 1) - { - ArrayList seqsMap = new ArrayList(); - for (SequenceI seq : sequences) - { - seqsMap.add(new SequenceI[] { seq }); - } - SequenceI[][] collatedSeqs = seqsMap.toArray(new SequenceI[0][0]); + if (pdbEntriesToView.length > 1) + { + ArrayList seqsMap = new ArrayList(); + for (SequenceI seq : sequences) + { + seqsMap.add(new SequenceI[] { seq }); + } + SequenceI[][] collatedSeqs = seqsMap.toArray(new SequenceI[0][0]); ssm.setProgressBar(null); ssm.setProgressBar("Fetching PDB Structures for selected entries.."); - sViewer.viewStructures(pdbEntriesToView, collatedSeqs, alignPanel); - } - else - { + sViewer.viewStructures(pdbEntriesToView, collatedSeqs, alignPanel); + } + else + { ssm.setProgressBar(null); ssm.setProgressBar("Fetching PDB Structure for " + pdbEntriesToView[0].getId()); - sViewer.viewStructures(pdbEntriesToView[0], sequences, alignPanel); - } + sViewer.viewStructures(pdbEntriesToView[0], sequences, alignPanel); + } } /** @@ -943,6 +947,9 @@ public class StructureChooser extends GStructureChooser implements isValidPBDEntry = false; if (txt_search.getText().length() > 0) { + String searchTerm = txt_search.getText().toLowerCase(); + searchTerm = searchTerm.split(":")[0]; + System.out.println(">>>>> search term : " + searchTerm); List wantedFields = new ArrayList(); FTSRestRequest pdbRequest = new FTSRestRequest(); pdbRequest.setAllowEmptySeq(false); @@ -950,7 +957,7 @@ public class StructureChooser extends GStructureChooser implements pdbRequest.setFieldToSearchBy("(pdb_id:"); pdbRequest.setWantedFields(wantedFields); pdbRequest - .setSearchTerm(txt_search.getText().toLowerCase() + ")"); +.setSearchTerm(searchTerm + ")"); pdbRequest.setAssociatedSequence(selectedSequence); pdbRestCleint = PDBFTSRestClient.getInstance(); wantedFields.add(pdbRestCleint.getPrimaryKeyColumn()); diff --git a/src/jalview/gui/TreePanel.java b/src/jalview/gui/TreePanel.java index 9522144..d78350d 100755 --- a/src/jalview/gui/TreePanel.java +++ b/src/jalview/gui/TreePanel.java @@ -161,6 +161,7 @@ public class TreePanel extends GTreePanel av.addPropertyChangeListener(new java.beans.PropertyChangeListener() { + @Override public void propertyChange(PropertyChangeEvent evt) { if (evt.getPropertyName().equals("alignment")) @@ -196,6 +197,7 @@ public class TreePanel extends GTreePanel } + @Override public void viewMenu_menuSelected() { buildAssociatedViewMenu(); @@ -231,6 +233,7 @@ public class TreePanel extends GTreePanel buttonGroup.add(item); item.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent evt) { treeCanvas.applyToAllViews = false; @@ -249,6 +252,7 @@ public class TreePanel extends GTreePanel itemf.setSelected(treeCanvas.applyToAllViews); itemf.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent evt) { treeCanvas.applyToAllViews = itemf.isSelected(); @@ -276,6 +280,7 @@ public class TreePanel extends GTreePanel } } + @Override public void run() { @@ -389,6 +394,7 @@ public class TreePanel extends GTreePanel * @param e * DOCUMENT ME! */ + @Override public void textbox_actionPerformed(ActionEvent e) { CutAndPasteTransfer cap = new CutAndPasteTransfer(); @@ -434,6 +440,7 @@ public class TreePanel extends GTreePanel * @param e * DOCUMENT ME! */ + @Override public void saveAsNewick_actionPerformed(ActionEvent e) { JalviewFileChooser chooser = new JalviewFileChooser( @@ -474,12 +481,14 @@ public class TreePanel extends GTreePanel * @param e * DOCUMENT ME! */ + @Override public void printMenu_actionPerformed(ActionEvent e) { // Putting in a thread avoids Swing painting problems treeCanvas.startPrinting(); } + @Override public void originalSeqData_actionPerformed(ActionEvent e) { if (!tree.hasOriginalSequenceData()) @@ -547,6 +556,7 @@ public class TreePanel extends GTreePanel * @param e * DOCUMENT ME! */ + @Override public void fitToWindow_actionPerformed(ActionEvent e) { treeCanvas.fitToWindow = fitToWindow.isSelected(); @@ -637,6 +647,7 @@ public class TreePanel extends GTreePanel * @param e * DOCUMENT ME! */ + @Override public void font_actionPerformed(ActionEvent e) { if (treeCanvas == null) @@ -666,6 +677,7 @@ public class TreePanel extends GTreePanel * @param e * DOCUMENT ME! */ + @Override public void distanceMenu_actionPerformed(ActionEvent e) { treeCanvas.setShowDistances(distanceMenu.isSelected()); @@ -677,6 +689,7 @@ public class TreePanel extends GTreePanel * @param e * DOCUMENT ME! */ + @Override public void bootstrapMenu_actionPerformed(ActionEvent e) { treeCanvas.setShowBootstrap(bootstrapMenu.isSelected()); @@ -688,6 +701,7 @@ public class TreePanel extends GTreePanel * @param e * DOCUMENT ME! */ + @Override public void placeholdersMenu_actionPerformed(ActionEvent e) { treeCanvas.setMarkPlaceholders(placeholdersMenu.isSelected()); @@ -699,6 +713,7 @@ public class TreePanel extends GTreePanel * @param e * DOCUMENT ME! */ + @Override public void epsTree_actionPerformed(ActionEvent e) { boolean accurateText = true; @@ -772,6 +787,7 @@ public class TreePanel extends GTreePanel * @param e * DOCUMENT ME! */ + @Override public void pngTree_actionPerformed(ActionEvent e) { int width = treeCanvas.getWidth(); @@ -828,6 +844,7 @@ public class TreePanel extends GTreePanel tree.applyToNodes(new NodeTransformI() { + @Override public void transform(BinaryNode node) { if (node instanceof SequenceNode diff --git a/src/jalview/io/HtmlSvgOutput.java b/src/jalview/io/HtmlSvgOutput.java index e554b8e..00af242 100644 --- a/src/jalview/io/HtmlSvgOutput.java +++ b/src/jalview/io/HtmlSvgOutput.java @@ -124,7 +124,7 @@ public class HtmlSvgOutput } } - if (renderStyle.equalsIgnoreCase("lineart")) + if (renderStyle.equalsIgnoreCase("Lineart")) { g1.setRenderingHint(SVGHints.KEY_DRAW_STRING_TYPE, SVGHints.VALUE_DRAW_STRING_TYPE_VECTOR); diff --git a/src/jalview/jbgui/GPreferences.java b/src/jalview/jbgui/GPreferences.java index c4c737c..25727d0 100755 --- a/src/jalview/jbgui/GPreferences.java +++ b/src/jalview/jbgui/GPreferences.java @@ -201,7 +201,7 @@ public class GPreferences extends JPanel /* * Output tab components */ - protected JComboBox epsRendering = new JComboBox(); + protected JComboBox @@ -7360,6 +7412,7 @@ and any path to a file to read from that file]]>