X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAlignFrame.java;h=f830fe68bd48c9babf5694da6630a6d166fe9978;hb=c075b7f23933cbb3c6b1dda53d249d8cbefbe0b6;hp=40fbd6d25853ebfeddb6d3ac016abddf724e8b06;hpb=0b1c761dfaa8242f122cf868e8897a06ec6eb727;p=jalview.git diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java index 40fbd6d..f830fe6 100644 --- a/src/jalview/appletgui/AlignFrame.java +++ b/src/jalview/appletgui/AlignFrame.java @@ -49,7 +49,9 @@ import jalview.datamodel.SequenceGroup; import jalview.datamodel.SequenceI; import jalview.io.AnnotationFile; import jalview.io.AppletFormatAdapter; +import jalview.io.DataSourceType; import jalview.io.FeaturesFile; +import jalview.io.FileFormat; import jalview.io.TCoffeeScoreFile; import jalview.schemes.Blosum62ColourScheme; import jalview.schemes.BuriedColourScheme; @@ -102,7 +104,6 @@ import java.net.URLEncoder; import java.util.Arrays; import java.util.Deque; import java.util.HashMap; -import java.util.Hashtable; import java.util.List; import java.util.Map; import java.util.StringTokenizer; @@ -219,6 +220,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, { viewport.setColumnSelection(columnSelection); } + viewport.setScaleAboveWrapped(scaleAbove.getState()); alignPanel = new AlignmentPanel(this, viewport); avc = new jalview.controller.AlignViewController(this, viewport, @@ -345,7 +347,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, * is protocol for accessing data referred to by file */ - public boolean parseFeaturesFile(String file, String type) + public boolean parseFeaturesFile(String file, DataSourceType type) { return parseFeaturesFile(file, type, true); } @@ -355,28 +357,25 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, * * @param file * file URL, content, or other resolvable path - * @param type + * @param sourceType * is protocol for accessing data referred to by file * @param autoenabledisplay * when true, display features flag will be automatically enabled if * features are loaded * @return true if data parsed as a features file */ - public boolean parseFeaturesFile(String file, String type, + public boolean parseFeaturesFile(String file, DataSourceType sourceType, boolean autoenabledisplay) { - // TODO: test if importing a features file onto an alignment which already - // has features with links overwrites the original links. - - Hashtable featureLinks = new Hashtable(); boolean featuresFile = false; try { - featuresFile = new jalview.io.FeaturesFile(file, type).parse(viewport - .getAlignment(), alignPanel.seqPanel.seqCanvas - .getFeatureRenderer().getFeatureColours(), featureLinks, - true, viewport.applet.getDefaultParameter("relaxedidmatch", - false)); + Map colours = alignPanel.seqPanel.seqCanvas + .getFeatureRenderer().getFeatureColours(); + boolean relaxedIdMatching = viewport.applet.getDefaultParameter( + "relaxedidmatch", false); + featuresFile = new FeaturesFile(file, sourceType).parse( + viewport.getAlignment(), colours, true, relaxedIdMatching); } catch (Exception ex) { ex.printStackTrace(); @@ -384,10 +383,6 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, if (featuresFile) { - if (featureLinks.size() > 0) - { - alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featureLinks = featureLinks; - } if (autoenabledisplay) { viewport.setShowSequenceFeatures(true); @@ -709,9 +704,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, // Hide everything by the current selection - this is a hack - we do the // invert and then hide // first check that there will be visible columns after the invert. - if ((viewport.getColumnSelection() != null - && viewport.getColumnSelection().getSelected() != null && viewport - .getColumnSelection().getSelected().size() > 0) + if (viewport.hasSelectedColumns() || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg .getEndRes())) { @@ -739,8 +732,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, hide = true; viewport.hideAllSelectedSeqs(); } - else if (!(toggleCols && viewport.getColumnSelection().getSelected() - .size() > 0)) + else if (!(toggleCols && viewport.hasSelectedColumns())) { viewport.showAllHiddenSeqs(); } @@ -748,7 +740,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, if (toggleCols) { - if (viewport.getColumnSelection().getSelected().size() > 0) + if (viewport.hasSelectedColumns()) { viewport.hideSelectedColumns(); if (!toggleSeqs) @@ -935,11 +927,11 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, if (alignPanel.getAlignment().getAlignmentAnnotation() != null) { for (AlignmentAnnotation aa : alignPanel.getAlignment() - .getAlignmentAnnotation()) - { - boolean visible = (aa.sequenceRef == null ? showForAlignment - : showForSequences); - aa.visible = visible; + .getAlignmentAnnotation()) + { + boolean visible = (aa.sequenceRef == null ? showForAlignment + : showForSequences); + aa.visible = visible; } } alignPanel.validateAnnotationDimensions(true); @@ -1366,13 +1358,13 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this); Frame frame = new Frame(); frame.add(cap); - jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage( + JalviewLite.addFrame(frame, MessageManager.formatMessage( "label.alignment_output_command", new Object[] { e.getActionCommand() }), 600, 500); - FeatureRenderer fr = this.alignPanel.cloneFeatureRenderer(); + FileFormat fileFormat = FileFormat.valueOf(e.getActionCommand()); cap.setText(new AppletFormatAdapter(alignPanel).formatSequences( - e.getActionCommand(), viewport.getAlignment(), + fileFormat, viewport.getAlignment(), viewport.getShowJVSuffix())); } @@ -1421,15 +1413,15 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, public String outputFeatures(boolean displayTextbox, String format) { String features; + FeaturesFile formatter = new FeaturesFile(); if (format.equalsIgnoreCase("Jalview")) { - features = new FeaturesFile().printJalviewFormat(viewport - .getAlignment().getSequencesArray(), - getDisplayedFeatureCols()); + features = formatter.printJalviewFormat(viewport.getAlignment() + .getSequencesArray(), getDisplayedFeatureCols()); } else { - features = new FeaturesFile().printGFFFormat(viewport.getAlignment() + features = formatter.printGffFormat(viewport.getAlignment() .getSequencesArray(), getDisplayedFeatureCols()); } @@ -2239,7 +2231,10 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, } sg.setEndRes(viewport.getAlignment().getWidth() - 1); viewport.setSelectionGroup(sg); - alignPanel.paintAlignment(true); + // JAL-2034 - should delegate to + // alignPanel to decide if overview needs + // updating. + alignPanel.paintAlignment(false); PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId()); viewport.sendSelection(); } @@ -2256,7 +2251,10 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, viewport.setSelectionGroup(null); alignPanel.idPanel.idCanvas.searchResults = null; alignPanel.seqPanel.seqCanvas.highlightSearchResults(null); - alignPanel.paintAlignment(true); + // JAL-2034 - should delegate to + // alignPanel to decide if overview needs + // updating. + alignPanel.paintAlignment(false); PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId()); viewport.sendSelection(); } @@ -3238,11 +3236,9 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, inputText.addActionListener(this); Menu outputTextboxMenu = new Menu( MessageManager.getString("label.out_to_textbox")); - for (int i = 0; i < jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS.length; i++) + for (String ff : FileFormat.getWritableFormats(true)) { - - MenuItem item = new MenuItem( - jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS[i]); + MenuItem item = new MenuItem(ff); item.addActionListener(new java.awt.event.ActionListener() { @@ -3516,10 +3512,10 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, nucleotideColour.setLabel(MessageManager.getString("label.nucleotide")); nucleotideColour.addActionListener(this); modifyPID.setLabel(MessageManager - .getString("label.modify_identity_thereshold")); + .getString("label.modify_identity_threshold")); modifyPID.addActionListener(this); modifyConservation.setLabel(MessageManager - .getString("label.modify_conservation_thereshold")); + .getString("label.modify_conservation_threshold")); modifyConservation.addActionListener(this); annotationColour.setLabel(MessageManager .getString("action.by_annotation")); @@ -4020,19 +4016,15 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, } // resolve data source // TODO: this code should be a refactored to an io package - String protocol = AppletFormatAdapter.resolveProtocol(pdbFile, "PDB"); + DataSourceType protocol = AppletFormatAdapter.resolveProtocol( + pdbFile, FileFormat.PDB); if (protocol == null) { return false; } if (needtoadd) { - // make a note of the access mode and add - if (pdbentry.getProperty() == null) - { - pdbentry.setProperty(new Hashtable()); - } - pdbentry.getProperty().put("protocol", protocol); + pdbentry.setProperty("protocol", protocol); toaddpdb.addPDBId(pdbentry); alignPanel.getStructureSelectionManager() .registerPDBEntry(pdbentry); @@ -4069,7 +4061,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, } public void newStructureView(JalviewLite applet, PDBEntry pdb, - SequenceI[] seqs, String[] chains, String protocol) + SequenceI[] seqs, String[] chains, DataSourceType protocol) { // Scrub any null sequences from the array Object[] sqch = cleanSeqChainArrays(seqs, chains); @@ -4080,10 +4072,16 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, System.err .println("JalviewLite.AlignFrame:newStructureView: No sequence to bind structure to."); } - if (protocol == null || protocol.trim().length() == 0 - || protocol.equals("null")) + if (protocol == null) { - protocol = (String) pdb.getProperty().get("protocol"); + String sourceType = (String) pdb.getProperty("protocol"); + try + { + protocol = DataSourceType.valueOf(sourceType); + } catch (IllegalArgumentException e) + { + // ignore + } if (protocol == null) { System.err.println("Couldn't work out protocol to open structure: " @@ -4106,12 +4104,11 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, { // can only do alignments with Jmol // find the last jmol window assigned to this alignment - jalview.appletgui.AppletJmol ajm = null, tajm; - Vector jmols = applet - .getAppletWindow(jalview.appletgui.AppletJmol.class); + AppletJmol ajm = null, tajm; + Vector jmols = applet.getAppletWindow(AppletJmol.class); for (int i = 0, iSize = jmols.size(); i < iSize; i++) { - tajm = (jalview.appletgui.AppletJmol) jmols.elementAt(i); + tajm = (AppletJmol) jmols.elementAt(i); if (tajm.ap.alignFrame == this) { ajm = tajm; @@ -4130,7 +4127,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, // otherwise, create a new window if (applet.jmolAvailable) { - new jalview.appletgui.AppletJmol(pdb, seqs, chains, alignPanel, + new AppletJmol(pdb, seqs, chains, alignPanel, protocol); applet.lastFrameX += 40; applet.lastFrameY += 40;