X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAlignFrame.java;h=fb1ee921fb60d63be72261c363909a294ccde9af;hb=d065bc916cb63af83cdab7319f5177a855724aba;hp=9d19ec819b5a8ce8989e94d1a4246efc055b4a3c;hpb=b0f76adef2787dd14566525e66a4073278e75d67;p=jalview.git diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java index 9d19ec8..fb1ee92 100644 --- a/src/jalview/appletgui/AlignFrame.java +++ b/src/jalview/appletgui/AlignFrame.java @@ -22,7 +22,9 @@ package jalview.appletgui; import jalview.analysis.AlignmentSorter; import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder; -import jalview.analysis.NJTree; +import jalview.analysis.TreeBuilder; +import jalview.analysis.scoremodels.PIDModel; +import jalview.analysis.scoremodels.ScoreModels; import jalview.api.AlignViewControllerGuiI; import jalview.api.AlignViewControllerI; import jalview.api.AlignViewportI; @@ -44,6 +46,7 @@ import jalview.datamodel.AlignmentAnnotation; import jalview.datamodel.AlignmentI; import jalview.datamodel.AlignmentOrder; import jalview.datamodel.ColumnSelection; +import jalview.datamodel.HiddenColumns; import jalview.datamodel.PDBEntry; import jalview.datamodel.Sequence; import jalview.datamodel.SequenceGroup; @@ -170,14 +173,14 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, } public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs, - ColumnSelection columnSelection, JalviewLite applet, + HiddenColumns hidden, JalviewLite applet, String title, boolean embedded) { - this(al, hiddenSeqs, columnSelection, applet, title, embedded, true); + this(al, hiddenSeqs, hidden, applet, title, embedded, true); } public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs, - ColumnSelection columnSelection, JalviewLite applet, + HiddenColumns hidden, JalviewLite applet, String title, boolean embedded, boolean addToDisplay) { if (applet != null) @@ -220,9 +223,9 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, { viewport.hideSequence(hiddenSeqs); } - if (columnSelection != null) + if (hidden != null) { - viewport.setColumnSelection(columnSelection); + viewport.getAlignment().setHiddenColumns(hidden); } viewport.setScaleAboveWrapped(scaleAbove.getState()); @@ -598,24 +601,22 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, case KeyEvent.VK_PAGE_UP: if (viewport.getWrapAlignment()) { - alignPanel.scrollUp(true); + ranges.scrollUp(true); } else { - alignPanel.setScrollValues(ranges.getStartRes(), - 2 * ranges.getStartSeq() - ranges.getEndSeq()); + ranges.pageUp(); } break; case KeyEvent.VK_PAGE_DOWN: if (viewport.getWrapAlignment()) { - alignPanel.scrollUp(false); + ranges.scrollUp(false); } else { - alignPanel - .setScrollValues(ranges.getStartRes(), ranges.getEndSeq()); + ranges.pageDown(); } break; @@ -1072,6 +1073,14 @@ 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(); @@ -1429,6 +1438,17 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, return null; } + private List getDisplayedFeatureGroups() + { + if (alignPanel.getFeatureRenderer() != null + && viewport.getFeaturesDisplayed() != null) + { + return alignPanel.getFeatureRenderer().getDisplayedFeatureGroups(); + + } + return null; + } + public String outputFeatures(boolean displayTextbox, String format) { String features; @@ -1436,12 +1456,14 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, if (format.equalsIgnoreCase("Jalview")) { features = formatter.printJalviewFormat(viewport.getAlignment() - .getSequencesArray(), getDisplayedFeatureCols()); + .getSequencesArray(), getDisplayedFeatureCols(), + getDisplayedFeatureGroups(), true); } else { features = formatter.printGffFormat(viewport.getAlignment() - .getSequencesArray(), getDisplayedFeatureCols()); + .getSequencesArray(), getDisplayedFeatureCols(), + getDisplayedFeatureGroups(), true); } if (displayTextbox) @@ -1789,7 +1811,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, synchronized void slideSequences(boolean right, int size) { - List sg = new Vector(); + List sg = new Vector<>(); if (viewport.cursorMode) { sg.add(viewport.getAlignment().getSequenceAt( @@ -1891,7 +1913,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, static StringBuffer copiedSequences; - static Vector copiedHiddenColumns; + static Vector copiedHiddenColumns; protected void copy_actionPerformed() { @@ -1902,7 +1924,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, SequenceGroup sg = viewport.getSelectionGroup(); copiedSequences = new StringBuffer(); - Map orderedSeqs = new HashMap(); + Map orderedSeqs = new HashMap<>(); for (int i = 0; i < sg.getSize(); i++) { SequenceI seq = sg.getSequenceAt(i); @@ -1915,12 +1937,13 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, if (viewport.hasHiddenColumns() && viewport.getSelectionGroup() != null) { - copiedHiddenColumns = new Vector(); + copiedHiddenColumns = new Vector<>(viewport.getAlignment() + .getHiddenColumns().getHiddenColumnsCopy()); int hiddenOffset = viewport.getSelectionGroup().getStartRes(); - for (int[] region : viewport.getColumnSelection().getHiddenColumns()) + for (int[] region : copiedHiddenColumns) { - copiedHiddenColumns.addElement(new int[] { - region[0] - hiddenOffset, region[1] - hiddenOffset }); + region[0] = region[0] - hiddenOffset; + region[1] = region[1] - hiddenOffset; } } else @@ -2035,7 +2058,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, { for (int i = 0; i < copiedHiddenColumns.size(); i++) { - int[] region = (int[]) copiedHiddenColumns.elementAt(i); + int[] region = copiedHiddenColumns.elementAt(i); af.viewport.hideColumns(region[0], region[1]); } } @@ -2682,9 +2705,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, boolean selected = conservationMenuItem.getState(); modifyConservation.setEnabled(selected); viewport.setConservationSelected(selected); - - // viewport.setAbovePIDThreshold(false); - // abovePIDThreshold.setState(false); + viewport.getResidueShading().setConservationApplied(selected); changeColour(viewport.getGlobalColourScheme()); @@ -2703,8 +2724,11 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, boolean selected = abovePIDThreshold.getState(); modifyPID.setEnabled(selected); viewport.setAbovePIDThreshold(selected); - // conservationMenuItem.setState(false); - // viewport.setConservationSelected(false); + if (!selected) + { + viewport.getResidueShading().setThreshold(0, + viewport.isIgnoreGapsConsensus()); + } changeColour(viewport.getGlobalColourScheme()); @@ -2814,29 +2838,31 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, public void averageDistanceTreeMenuItem_actionPerformed() { - NewTreePanel(NJTree.AVERAGE_DISTANCE, "PID", + newTreePanel(TreeBuilder.AVERAGE_DISTANCE, new PIDModel().getName(), "Average distance tree using PID"); } public void neighbourTreeMenuItem_actionPerformed() { - NewTreePanel(NJTree.NEIGHBOUR_JOINING, "PID", + newTreePanel(TreeBuilder.NEIGHBOUR_JOINING, new PIDModel().getName(), "Neighbour joining tree using PID"); } protected void njTreeBlosumMenuItem_actionPerformed() { - NewTreePanel(NJTree.NEIGHBOUR_JOINING, "BL", + newTreePanel(TreeBuilder.NEIGHBOUR_JOINING, ScoreModels.getInstance() + .getBlosum62().getName(), "Neighbour joining tree using BLOSUM62"); } protected void avTreeBlosumMenuItem_actionPerformed() { - NewTreePanel(NJTree.AVERAGE_DISTANCE, "BL", + newTreePanel(TreeBuilder.AVERAGE_DISTANCE, ScoreModels.getInstance() + .getBlosum62().getName(), "Average distance tree using BLOSUM62"); } - void NewTreePanel(String type, String pwType, String title) + void newTreePanel(String type, String pwType, String title) { // are the sequences aligned? if (!viewport.getAlignment().isAligned(false)) @@ -3342,7 +3368,10 @@ 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); @@ -4191,9 +4220,10 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, * @param csel * - columns to be selected on the alignment */ - public void select(SequenceGroup sel, ColumnSelection csel) + public void select(SequenceGroup sel, ColumnSelection csel, + HiddenColumns hidden) { - alignPanel.seqPanel.selection(sel, csel, null); + alignPanel.seqPanel.selection(sel, csel, hidden, null); } public void scrollTo(int row, int column)