X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAlignFrame.java;h=2646edebaa67bfffded1fc8b276fc73611851144;hb=c9e79462a42264c560a828808934a3a156c39d0c;hp=511a2640bd420c8da6d0b0b4a8bfef5e751f6973;hpb=e838644df5d5a10a16cf0ad7fb23d24dd7d2729a;p=jalview.git diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java index 511a264..2646ede 100644 --- a/src/jalview/appletgui/AlignFrame.java +++ b/src/jalview/appletgui/AlignFrame.java @@ -49,7 +49,11 @@ 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.FileFormatI; +import jalview.io.FileFormats; import jalview.io.TCoffeeScoreFile; import jalview.schemes.Blosum62ColourScheme; import jalview.schemes.BuriedColourScheme; @@ -60,7 +64,7 @@ import jalview.schemes.HydrophobicColourScheme; import jalview.schemes.NucleotideColourScheme; import jalview.schemes.PIDColourScheme; import jalview.schemes.PurinePyrimidineColourScheme; -import jalview.schemes.RNAHelicesColourChooser; +import jalview.schemes.RNAHelicesColour; import jalview.schemes.StrandColourScheme; import jalview.schemes.TCoffeeColourScheme; import jalview.schemes.TaylorColourScheme; @@ -71,6 +75,7 @@ import jalview.structures.models.AAStructureBindingModel; import jalview.util.MappingUtils; import jalview.util.MessageManager; import jalview.viewmodel.AlignmentViewport; +import jalview.viewmodel.ViewportRanges; import java.awt.BorderLayout; import java.awt.Canvas; @@ -280,6 +285,16 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, } if (viewport.getAlignment().isNucleotide()) { + conservationMenuItem.setEnabled(false); + clustalColour.setEnabled(false); + BLOSUM62Colour.setEnabled(false); + zappoColour.setEnabled(false); + taylorColour.setEnabled(false); + hydrophobicityColour.setEnabled(false); + helixColour.setEnabled(false); + strandColour.setEnabled(false); + turnColour.setEnabled(false); + buriedColour.setEnabled(false); viewport.updateStrucConsensus(alignPanel); if (viewport.getAlignment().hasRNAStructure()) { @@ -294,6 +309,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, { RNAHelixColour.setEnabled(false); purinePyrimidineColour.setEnabled(false); + nucleotideColour.setEnabled(false); } // Some JVMS send keyevents to Top frame or lowest panel, // Havent worked out why yet. So add to both this frame and seqCanvas for @@ -345,7 +361,7 @@ 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); } @@ -355,14 +371,14 @@ 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) { boolean featuresFile = false; @@ -372,7 +388,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, .getFeatureRenderer().getFeatureColours(); boolean relaxedIdMatching = viewport.applet.getDefaultParameter( "relaxedidmatch", false); - featuresFile = new FeaturesFile(file, type).parse( + featuresFile = new FeaturesFile(file, sourceType).parse( viewport.getAlignment(), colours, true, relaxedIdMatching); } catch (Exception ex) { @@ -405,6 +421,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, @Override public void keyPressed(KeyEvent evt) { + ViewportRanges ranges = viewport.getRanges(); + if (viewport.cursorMode && ((evt.getKeyCode() >= KeyEvent.VK_0 && evt.getKeyCode() <= KeyEvent.VK_9) || (evt .getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt @@ -556,8 +574,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, new String[] { (viewport.cursorMode ? "on" : "off") })); if (viewport.cursorMode) { - alignPanel.seqPanel.seqCanvas.cursorX = viewport.startRes; - alignPanel.seqPanel.seqCanvas.cursorY = viewport.startSeq; + alignPanel.seqPanel.seqCanvas.cursorX = ranges.getStartRes(); + alignPanel.seqPanel.seqCanvas.cursorY = ranges.getStartSeq(); } break; @@ -583,8 +601,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, } else { - alignPanel.setScrollValues(viewport.startRes, viewport.startSeq - - viewport.endSeq + viewport.startSeq); + alignPanel.setScrollValues(ranges.getStartRes(), + 2 * ranges.getStartSeq() - ranges.getEndSeq()); } break; @@ -595,8 +613,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, } else { - alignPanel.setScrollValues(viewport.startRes, viewport.startSeq - + viewport.endSeq - viewport.startSeq); + alignPanel + .setScrollValues(ranges.getStartRes(), ranges.getEndSeq()); } break; @@ -925,11 +943,11 @@ 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); @@ -1053,6 +1071,14 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, { delete_actionPerformed(); } + else if (source == createGroup) + { + createGroup_actionPerformed(); + } + else if (source == unGroup) + { + unGroup_actionPerformed(); + } else if (source == grpsFromSelection) { makeGrpsFromSelection_actionPerformed(); @@ -1253,7 +1279,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, // } else if (source == RNAHelixColour) { - new RNAHelicesColourChooser(viewport, alignPanel); + changeColour(new RNAHelicesColour(viewport.getAlignment())); + // new RNAHelicesColourChooser(viewport, alignPanel); } else if (source == modifyPID) { @@ -1356,13 +1383,14 @@ 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(); + FileFormatI fileFormat = FileFormats.getInstance().forName( + e.getActionCommand()); cap.setText(new AppletFormatAdapter(alignPanel).formatSequences( - e.getActionCommand(), viewport.getAlignment(), + fileFormat, viewport.getAlignment(), viewport.getShowJVSuffix())); } @@ -1414,9 +1442,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, FeaturesFile formatter = new FeaturesFile(); if (format.equalsIgnoreCase("Jalview")) { - features = formatter.printJalviewFormat(viewport - .getAlignment().getSequencesArray(), - getDisplayedFeatureCols()); + features = formatter.printJalviewFormat(viewport.getAlignment() + .getSequencesArray(), getDisplayedFeatureCols()); } else { @@ -1479,10 +1506,13 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, url.append(appendProtocol(viewport.applet.getParameter("annotations"))); } - if (viewport.applet.getParameter("jnetfile") != null) + if (viewport.applet.getParameter("jnetfile") != null + || viewport.applet.getParameter("jpredfile") != null) { url.append("&annotations="); - url.append(appendProtocol(viewport.applet.getParameter("jnetfile"))); + url.append(appendProtocol(viewport.applet.getParameter("jnetfile") != null ? viewport.applet + .getParameter("jnetfile") : viewport.applet + .getParameter("jpredfile"))); } if (viewport.applet.getParameter("defaultColour") != null) @@ -2044,7 +2074,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, seqs, 0, viewport.getAlignment().getWidth(), viewport.getAlignment())); - viewport.setEndSeq(viewport.getAlignment().getHeight()); + viewport.getRanges().setEndSeq(viewport.getAlignment().getHeight()); viewport.getAlignment().getWidth(); viewport.firePropertyChange("alignment", null, viewport.getAlignment() .getSequences()); @@ -2280,6 +2310,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, void trimAlignment(boolean trimLeft) { + AlignmentI al = viewport.getAlignment(); + ViewportRanges ranges = viewport.getRanges(); ColumnSelection colSel = viewport.getColumnSelection(); int column; @@ -2302,20 +2334,20 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, } else { - seqs = viewport.getAlignment().getSequencesArray(); + seqs = al.getSequencesArray(); } TrimRegionCommand trimRegion; if (trimLeft) { trimRegion = new TrimRegionCommand("Remove Left", true, seqs, - column, viewport.getAlignment()); - viewport.setStartRes(0); + column, al); + ranges.setStartRes(0); } else { trimRegion = new TrimRegionCommand("Remove Right", false, seqs, - column, viewport.getAlignment()); + column, al); } statusBar.setText(MessageManager.formatMessage( @@ -2324,23 +2356,25 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, .toString() })); addHistoryItem(trimRegion); - for (SequenceGroup sg : viewport.getAlignment().getGroups()) + for (SequenceGroup sg : al.getGroups()) { if ((trimLeft && !sg.adjustForRemoveLeft(column)) || (!trimLeft && !sg.adjustForRemoveRight(column))) { - viewport.getAlignment().deleteGroup(sg); + al.deleteGroup(sg); } } - viewport.firePropertyChange("alignment", null, viewport - .getAlignment().getSequences()); + viewport.firePropertyChange("alignment", null, al.getSequences()); } } public void removeGappedColumnMenuItem_actionPerformed() { - int start = 0, end = viewport.getAlignment().getWidth() - 1; + AlignmentI al = viewport.getAlignment(); + ViewportRanges ranges = viewport.getRanges(); + int start = 0; + int end = ranges.getAbsoluteAlignmentWidth() - 1; SequenceI[] seqs; if (viewport.getSelectionGroup() != null) @@ -2368,22 +2402,24 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, // This is to maintain viewport position on first residue // of first sequence - SequenceI seq = viewport.getAlignment().getSequenceAt(0); - int startRes = seq.findPosition(viewport.startRes); + SequenceI seq = al.getSequenceAt(0); + int startRes = seq.findPosition(ranges.getStartRes()); // ShiftList shifts; // viewport.getAlignment().removeGaps(shifts=new ShiftList()); // edit.alColumnChanges=shifts.getInverse(); // if (viewport.hasHiddenColumns) // viewport.getColumnSelection().compensateForEdits(shifts); - viewport.setStartRes(seq.findIndex(startRes) - 1); - viewport.firePropertyChange("alignment", null, viewport.getAlignment() - .getSequences()); + ranges.setStartRes(seq.findIndex(startRes) - 1); + viewport.firePropertyChange("alignment", null, al.getSequences()); } public void removeAllGapsMenuItem_actionPerformed() { - int start = 0, end = viewport.getAlignment().getWidth() - 1; + AlignmentI al = viewport.getAlignment(); + ViewportRanges ranges = viewport.getRanges(); + int start = 0; + int end = ranges.getAbsoluteAlignmentWidth() - 1; SequenceI[] seqs; if (viewport.getSelectionGroup() != null) @@ -2400,16 +2436,15 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, // This is to maintain viewport position on first residue // of first sequence - SequenceI seq = viewport.getAlignment().getSequenceAt(0); - int startRes = seq.findPosition(viewport.startRes); + SequenceI seq = al.getSequenceAt(0); + int startRes = seq.findPosition(ranges.getStartRes()); addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end, - viewport.getAlignment())); + al)); - viewport.setStartRes(seq.findIndex(startRes) - 1); + ranges.setStartRes(seq.findIndex(startRes) - 1); - viewport.firePropertyChange("alignment", null, viewport.getAlignment() - .getSequences()); + viewport.firePropertyChange("alignment", null, al.getSequences()); } @@ -2622,26 +2657,6 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, @Override public void changeColour(ColourSchemeI cs) { - - if (cs != null) - { - if (viewport.getAbovePIDThreshold()) - { - viewport.setThreshold(SliderPanel.setPIDSliderSource(alignPanel, - cs, "Background")); - } - - if (viewport.getConservationSelected()) - { - cs.setConservationApplied(true); - viewport.setIncrement(SliderPanel.setConservationSlider(alignPanel, - cs, "Background")); - } - else - { - cs.setConservationApplied(false); - } - } viewport.setGlobalColourScheme(cs); alignPanel.paintAlignment(true); @@ -2653,7 +2668,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, && viewport.getGlobalColourScheme() != null) { SliderPanel.setPIDSliderSource(alignPanel, - viewport.getGlobalColourScheme(), "Background"); + viewport.getResidueShading(), alignPanel.getViewName()); SliderPanel.showPIDSlider(); } } @@ -2664,33 +2679,51 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, && viewport.getGlobalColourScheme() != null) { SliderPanel.setConservationSlider(alignPanel, - viewport.getGlobalColourScheme(), "Background"); + viewport.getResidueShading(), alignPanel.getViewName()); SliderPanel.showConservationSlider(); } } protected void conservationMenuItem_actionPerformed() { - viewport.setConservationSelected(conservationMenuItem.getState()); - - viewport.setAbovePIDThreshold(false); - abovePIDThreshold.setState(false); + boolean selected = conservationMenuItem.getState(); + modifyConservation.setEnabled(selected); + viewport.setConservationSelected(selected); + viewport.getResidueShading().setConservationApplied(selected); changeColour(viewport.getGlobalColourScheme()); - modifyConservation_actionPerformed(); + if (selected) + { + modifyConservation_actionPerformed(); + } + else + { + SliderPanel.hideConservationSlider(); + } } public void abovePIDThreshold_actionPerformed() { - viewport.setAbovePIDThreshold(abovePIDThreshold.getState()); - - conservationMenuItem.setState(false); - viewport.setConservationSelected(false); + boolean selected = abovePIDThreshold.getState(); + modifyPID.setEnabled(selected); + viewport.setAbovePIDThreshold(selected); + if (!selected) + { + viewport.getResidueShading().setThreshold(0, + viewport.isIgnoreGapsConsensus()); + } changeColour(viewport.getGlobalColourScheme()); - modifyPID_actionPerformed(); + if (selected) + { + modifyPID_actionPerformed(); + } + else + { + SliderPanel.hidePIDSlider(); + } } public void sortPairwiseMenuItem_actionPerformed() @@ -3235,11 +3268,9 @@ 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 : FileFormats.getInstance().getWritableFormats(true)) { - - MenuItem item = new MenuItem( - jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS[i]); + MenuItem item = new MenuItem(ff); item.addActionListener(new java.awt.event.ActionListener() { @@ -3315,7 +3346,10 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, .getString("action.make_groups_selection")); grpsFromSelection.addActionListener(this); createGroup.setLabel(MessageManager.getString("action.create_group")); + createGroup.addActionListener(this); unGroup.setLabel(MessageManager.getString("action.remove_group")); + unGroup.addActionListener(this); + annotationColumnSelection.setLabel(MessageManager .getString("action.select_by_annotation")); annotationColumnSelection.addActionListener(this); @@ -3437,7 +3471,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, .getString("label.colour_text")); colourTextMenuItem.addItemListener(this); displayNonconservedMenuItem.setLabel(MessageManager - .getString("label.show_non_conversed")); + .getString("label.show_non_conserved")); displayNonconservedMenuItem.addItemListener(this); wrapMenuItem.setLabel(MessageManager.getString("action.wrap")); wrapMenuItem.addItemListener(this); @@ -3460,45 +3494,50 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, .getString("label.apply_colour_to_all_groups")); applyToAllGroups.setState(true); applyToAllGroups.addItemListener(this); - clustalColour.setLabel(MessageManager.getString("label.clustalx")); + clustalColour.setLabel(MessageManager + .getString("label.colourScheme_clustal")); clustalColour.addActionListener(this); - zappoColour.setLabel(MessageManager.getString("label.zappo")); + zappoColour.setLabel(MessageManager + .getString("label.colourScheme_zappo")); zappoColour.addActionListener(this); - taylorColour.setLabel(MessageManager.getString("label.taylor")); + taylorColour.setLabel(MessageManager + .getString("label.colourScheme_taylor")); taylorColour.addActionListener(this); hydrophobicityColour.setLabel(MessageManager - .getString("label.hydrophobicity")); + .getString("label.colourScheme_hydrophobic")); hydrophobicityColour.addActionListener(this); - helixColour - .setLabel(MessageManager.getString("label.helix_propensity")); + helixColour.setLabel(MessageManager + .getString("label.colourScheme_helix_propensity")); helixColour.addActionListener(this); strandColour.setLabel(MessageManager - .getString("label.strand_propensity")); + .getString("label.colourScheme_strand_propensity")); strandColour.addActionListener(this); - turnColour.setLabel(MessageManager.getString("label.turn_propensity")); + turnColour.setLabel(MessageManager + .getString("label.colourScheme_turn_propensity")); turnColour.addActionListener(this); - buriedColour.setLabel(MessageManager.getString("label.buried_index")); + buriedColour.setLabel(MessageManager + .getString("label.colourScheme_buried_index")); buriedColour.addActionListener(this); purinePyrimidineColour.setLabel(MessageManager - .getString("label.purine_pyrimidine")); + .getString("label.colourScheme_purine/pyrimidine")); purinePyrimidineColour.addActionListener(this); // RNAInteractionColour.setLabel(MessageManager // .getString("label.rna_interaction")); // RNAInteractionColour.addActionListener(this); RNAHelixColour.setLabel(MessageManager - .getString("action.by_rna_helixes")); + .getString("label.colourScheme_rna_helices")); RNAHelixColour.addActionListener(this); userDefinedColour.setLabel(MessageManager .getString("action.user_defined")); userDefinedColour.addActionListener(this); PIDColour.setLabel(MessageManager - .getString("label.percentage_identity")); + .getString("label.colourScheme_%_identity")); PIDColour.addActionListener(this); BLOSUM62Colour.setLabel(MessageManager - .getString("label.blosum62_score")); + .getString("label.colourScheme_blosum62")); BLOSUM62Colour.addActionListener(this); - tcoffeeColour - .setLabel(MessageManager.getString("label.tcoffee_scores")); + tcoffeeColour.setLabel(MessageManager + .getString("label.colourScheme_t-coffee_scores")); // it will be enabled only if a score file is provided tcoffeeColour.setEnabled(false); tcoffeeColour.addActionListener(this); @@ -3510,13 +3549,16 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, abovePIDThreshold.setLabel(MessageManager .getString("label.above_identity_threshold")); abovePIDThreshold.addItemListener(this); - nucleotideColour.setLabel(MessageManager.getString("label.nucleotide")); + nucleotideColour.setLabel(MessageManager + .getString("label.colourScheme_nucleotide")); nucleotideColour.addActionListener(this); modifyPID.setLabel(MessageManager .getString("label.modify_identity_threshold")); + modifyPID.setEnabled(abovePIDThreshold.getState()); modifyPID.addActionListener(this); modifyConservation.setLabel(MessageManager .getString("label.modify_conservation_threshold")); + modifyConservation.setEnabled(conservationMenuItem.getState()); modifyConservation.addActionListener(this); annotationColour.setLabel(MessageManager .getString("action.by_annotation")); @@ -3550,7 +3592,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, .getString("label.neighbour_joining_identity")); neighbourTreeMenuItem.addActionListener(this); avDistanceTreeBlosumMenuItem.setLabel(MessageManager - .getString("label.average_distance_bloslum62")); + .getString("label.average_distance_blosum62")); avDistanceTreeBlosumMenuItem.addActionListener(this); njTreeBlosumMenuItem.setLabel(MessageManager .getString("label.neighbour_blosum62")); @@ -4017,7 +4059,8 @@ 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; @@ -4061,7 +4104,7 @@ 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); @@ -4072,10 +4115,16 @@ 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("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: " @@ -4098,12 +4147,11 @@ 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; @@ -4122,7 +4170,7 @@ 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;