X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignViewport.java;h=7ab84ad1002eb0b5539502807409cf44d71cc7d4;hb=f4b2472c686ae3ca2e19147f468c761b3eef0529;hp=05e446e7e3ebc47b3c19e41345cdb6fd892f5790;hpb=d0a3c7594380d978b0d3bf3cbdba55a016b9d920;p=jalview.git diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java index 05e446e..7ab84ad 100644 --- a/src/jalview/gui/AlignViewport.java +++ b/src/jalview/gui/AlignViewport.java @@ -73,6 +73,14 @@ import javax.swing.JInternalFrame; public class AlignViewport extends AlignmentViewport implements SelectionSource { + + public final static int NO_SPLIT = 0; + + public final static int SPLIT_FRAME = 1; + + public final static int NEW_WINDOW = 2; + + Font font; boolean cursorMode = false; @@ -162,7 +170,7 @@ public class AlignViewport extends AlignmentViewport * @param hiddenColumns * @param seqsetid * (may be null) - */ +f */ public AlignViewport(AlignmentI al, HiddenColumns hiddenColumns, String seqsetid) { @@ -215,7 +223,7 @@ public class AlignViewport extends AlignmentViewport setRightAlignIds(Cache.getDefault("RIGHT_ALIGN_IDS", false)); setCentreColumnLabels(Cache.getDefault("CENTRE_COLUMN_LABELS", false)); - autoCalculateConsensus = Cache.getDefault("AUTO_CALC_CONSENSUS", true); + autoCalculateConsensusAndConservation = Cache.getDefault("AUTO_CALC_CONSENSUS", true); setPadGaps(Cache.getDefault("PAD_GAPS", true)); setShowNPFeats(Cache.getDefault("SHOW_NPFEATS_TOOLTIP", true)); @@ -386,7 +394,7 @@ public class AlignViewport extends AlignmentViewport if (align != null) { StructureSelectionManager ssm = StructureSelectionManager - .getStructureSelectionManager(Desktop.instance); + .getStructureSelectionManager(Desktop.getInstance()); ssm.registerMappings(align.getCodonFrames()); } @@ -408,7 +416,7 @@ public class AlignViewport extends AlignmentViewport if (mappings != null) { StructureSelectionManager ssm = StructureSelectionManager - .getStructureSelectionManager(Desktop.instance); + .getStructureSelectionManager(Desktop.getInstance()); for (AlignedCodonFrame acf : mappings) { if (noReferencesTo(acf)) @@ -534,7 +542,7 @@ public class AlignViewport extends AlignmentViewport public void sendSelection() { jalview.structure.StructureSelectionManager - .getStructureSelectionManager(Desktop.instance) + .getStructureSelectionManager(Desktop.getInstance()) .sendSelection(new SequenceGroup(getSelectionGroup()), new ColumnSelection(getColumnSelection()), new HiddenColumns(getAlignment().getHiddenColumns()), @@ -580,7 +588,7 @@ public class AlignViewport extends AlignmentViewport public StructureSelectionManager getStructureSelectionManager() { return StructureSelectionManager - .getStructureSelectionManager(Desktop.instance); + .getStructureSelectionManager(Desktop.getInstance()); } @Override @@ -710,16 +718,20 @@ public class AlignViewport extends AlignmentViewport { if (AlignmentUtils.isMappable(toAdd, getAlignment())) { - if (openLinkedAlignment(toAdd, title)) - { - return; - } + openLinkedAlignment(toAdd, title); + return; } } + addDataToAlignment(toAdd); + } - /* - * No mappings, or offer declined - add sequences to this alignment - */ + /** + * adds sequences to this alignment + * + * @param toAdd + */ + void addDataToAlignment(AlignmentI toAdd) + { // TODO: JAL-407 regardless of above - identical sequences (based on ID and // provenance) should share the same dataset sequence @@ -741,8 +753,9 @@ public class AlignViewport extends AlignmentViewport } } - ranges.setEndSeq(getAlignment().getHeight()); - firePropertyChange("alignment", null, getAlignment().getSequences()); + ranges.setEndSeq(getAlignment().getHeight() - 1); // BH 2019.04.18 + notifyAlignment(); + } /** @@ -754,34 +767,69 @@ public class AlignViewport extends AlignmentViewport * @param al * @param title */ - protected boolean openLinkedAlignment(AlignmentI al, String title) + protected void openLinkedAlignment(AlignmentI al, String title) { String[] options = new String[] { MessageManager.getString("action.no"), MessageManager.getString("label.split_window"), MessageManager.getString("label.new_window"), }; final String question = JvSwingUtils.wrapTooltip(true, MessageManager.getString("label.open_split_window?")); - int response = JvOptionPane.showOptionDialog(Desktop.desktop, question, + final AlignViewport us = this; + + /* + * options No, Split Window, New Window correspond to + * dialog responses 0, 1, 2 (even though JOptionPane shows them + * in reverse order) + */ + JvOptionPane dialog = JvOptionPane.newOptionDialog(Desktop.getDesktopPane()) + .setResponseHandler(NO_SPLIT, new Runnable() + { + @Override + public void run() + { + addDataToAlignment(al); + } + }).setResponseHandler(SPLIT_FRAME, new Runnable() + { + @Override + public void run() + { + openLinkedAlignmentAs(getAlignPanel().alignFrame, + new Alignment(getAlignment()), al, title, + SPLIT_FRAME); +// us.openLinkedAlignmentAs(al, title, true); + } + }).setResponseHandler(NEW_WINDOW, new Runnable() + { + @Override + public void run() + { + openLinkedAlignmentAs(null, getAlignment(), al, title, + NEW_WINDOW); + } + }); + dialog.showDialog(question, MessageManager.getString("label.open_split_window"), JvOptionPane.DEFAULT_OPTION, JvOptionPane.PLAIN_MESSAGE, null, options, options[0]); - - if (response != 1 && response != 2) - { - return false; - } - final boolean openSplitPane = (response == 1); - final boolean openInNewWindow = (response == 2); - + } + /** + * Open a split frame or a new window + * + * @param al + * @param title + * @param mode + * SPLIT_FRAME or NEW_WINDOW + */ + public static void openLinkedAlignmentAs(AlignFrame thisFrame, + AlignmentI thisAlignment, AlignmentI al, String title, int mode) + { /* * Identify protein and dna alignments. Make a copy of this one if opening * in a new split pane. */ - AlignmentI thisAlignment = openSplitPane ? new Alignment(getAlignment()) - : getAlignment(); AlignmentI protein = al.isNucleotide() ? thisAlignment : al; - final AlignmentI cdna = al.isNucleotide() ? al : thisAlignment; - + AlignmentI cdna = al.isNucleotide() ? al : thisAlignment; /* * Map sequences. At least one should get mapped as we have already passed * the test for 'mappability'. Any mappings made will be added to the @@ -809,7 +857,7 @@ public class AlignViewport extends AlignmentViewport // alignFrame.setFileName(file, format); // } - if (openInNewWindow) + if (mode == NEW_WINDOW) { Desktop.addInternalFrame(newAlignFrame, title, AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT); @@ -823,13 +871,11 @@ public class AlignViewport extends AlignmentViewport { } - if (openSplitPane) + if (mode == SPLIT_FRAME) { al.alignAs(thisAlignment); - protein = openSplitFrame(newAlignFrame, thisAlignment); + openSplitFrame(thisFrame, newAlignFrame, thisAlignment); } - - return true; } /** @@ -842,8 +888,8 @@ public class AlignViewport extends AlignmentViewport * cdna/protein complement alignment to show in the other split half * @return the protein alignment in the split frame */ - protected AlignmentI openSplitFrame(AlignFrame newAlignFrame, - AlignmentI complement) + static protected AlignmentI openSplitFrame(AlignFrame thisFrame, + AlignFrame newAlignFrame, AlignmentI complement) { /* * Make a new frame with a copy of the alignment we are adding to. If this @@ -852,7 +898,8 @@ public class AlignViewport extends AlignmentViewport */ AlignFrame copyMe = new AlignFrame(complement, AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT); - copyMe.setTitle(getAlignPanel().alignFrame.getTitle()); + copyMe.setTitle(thisFrame.getTitle()); + AlignmentI al = newAlignFrame.viewport.getAlignment(); final AlignFrame proteinFrame = al.isNucleotide() ? copyMe @@ -1101,4 +1148,5 @@ public class AlignViewport extends AlignmentViewport { this.viewName = viewName; } + }