X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignFrame.java;h=a616dc036bfa51791c5468d07bba6814243beb26;hb=c70d42a1afc972ddb3757b9ec4cece3458d396a1;hp=88271b9505b574159d42bb32e9cde475583751c8;hpb=bfd019e68fc472cb1ac9a71e8118adc4eedc6609;p=jalview.git diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java index 88271b9..a616dc0 100644 --- a/src/jalview/gui/AlignFrame.java +++ b/src/jalview/gui/AlignFrame.java @@ -845,6 +845,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * operation that affects the data in the current view (selection changed, * etc) to update the menus to reflect the new state. */ + @Override public void setMenusForViewport() { setMenusFromViewport(viewport); @@ -1309,19 +1310,16 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, int startPos = aligmentStartEnd[0]; int endPos = aligmentStartEnd[1]; - int[] lowestRange = new int[2]; - int[] higestRange = new int[2]; + int[] lowestRange = new int[] { -1, -1 }; + int[] higestRange = new int[] { -1, -1 }; for (int[] hiddenCol : hiddenCols) { - // System.out.println("comparing : " + hiddenCol[0] + "-" + hiddenCol[1]); lowestRange = (hiddenCol[0] <= startPos) ? hiddenCol : lowestRange; higestRange = (hiddenCol[1] >= endPos) ? hiddenCol : higestRange; } - // System.out.println("min : " + lowestRange[0] + "-" + lowestRange[1]); - // System.out.println("max : " + higestRange[0] + "-" + higestRange[1]); - if (lowestRange[0] == 0 && lowestRange[1] == 0) + if (lowestRange[0] == -1 && lowestRange[1] == -1) { startPos = aligmentStartEnd[0]; } @@ -1330,27 +1328,27 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, startPos = lowestRange[1] + 1; } - if (higestRange[0] == 0 && higestRange[1] == 0) + if (higestRange[0] == -1 && higestRange[1] == -1) { endPos = aligmentStartEnd[1]; } else { - endPos = higestRange[0]; + endPos = higestRange[0] - 1; } - // System.out.println("Export range : " + minPos + " - " + maxPos); + // System.out.println("Export range : " + startPos + " - " + endPos); return new int[] { startPos, endPos }; } public static void main(String[] args) { ArrayList hiddenCols = new ArrayList(); - hiddenCols.add(new int[] { 0, 4 }); + hiddenCols.add(new int[] { 0, 0 }); hiddenCols.add(new int[] { 6, 9 }); hiddenCols.add(new int[] { 11, 12 }); hiddenCols.add(new int[] { 33, 33 }); - hiddenCols.add(new int[] { 45, 50 }); + hiddenCols.add(new int[] { 50, 50 }); int[] x = getStartEnd(new int[] { 0, 50 }, hiddenCols); // System.out.println("Export range : " + x[0] + " - " + x[1]); @@ -1371,7 +1369,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, @Override public void bioJSMenuItem_actionPerformed(ActionEvent e) { - BioJsHTMLOutput bjs = new BioJsHTMLOutput(alignPanel); + BioJsHTMLOutput bjs = new BioJsHTMLOutput(alignPanel, this); bjs.exportJalviewAlignmentAsBioJsHtmlFile(); } @@ -1404,6 +1402,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, alignPanel.makeEPS(f); } + @Override public void createSVG(File f) { alignPanel.makeSVG(f); @@ -1577,6 +1576,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } } + @Override public void addHistoryItem(CommandI command) { if (command.getSize() > 0) @@ -2375,20 +2375,24 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, */ if (sg.getSize() == viewport.getAlignment().getHeight()) { - int confirm = JOptionPane.showConfirmDialog(this, - MessageManager.getString("warn.delete_all"), // $NON-NLS-1$ - MessageManager.getString("label.delete_all"), // $NON-NLS-1$ - JOptionPane.OK_CANCEL_OPTION); - - if (confirm == JOptionPane.CANCEL_OPTION - || confirm == JOptionPane.CLOSED_OPTION) + boolean isEntireAlignWidth = (((sg.getEndRes() - sg.getStartRes()) + 1) == viewport + .getAlignment().getWidth()) ? true : false; + if (isEntireAlignWidth) { - return; + int confirm = JOptionPane.showConfirmDialog(this, + MessageManager.getString("warn.delete_all"), // $NON-NLS-1$ + MessageManager.getString("label.delete_all"), // $NON-NLS-1$ + JOptionPane.OK_CANCEL_OPTION); + + if (confirm == JOptionPane.CANCEL_OPTION + || confirm == JOptionPane.CLOSED_OPTION) + { + return; + } } viewport.getColumnSelection().removeElements(sg.getStartRes(), sg.getEndRes() + 1); } - SequenceI[] cut = sg.getSequences() .toArray(new SequenceI[sg.getSize()]); @@ -2543,7 +2547,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, ColumnSelection colSel = viewport.getColumnSelection(); int column; - if (colSel.size() > 0) + if (!colSel.isEmpty()) { if (trimLeft) { @@ -2568,18 +2572,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, TrimRegionCommand trimRegion; if (trimLeft) { - trimRegion = new TrimRegionCommand("Remove Left", - TrimRegionCommand.TRIM_LEFT, seqs, column, - viewport.getAlignment(), viewport.getColumnSelection(), - viewport.getSelectionGroup()); + trimRegion = new TrimRegionCommand("Remove Left", true, seqs, + column, viewport.getAlignment()); viewport.setStartRes(0); } else { - trimRegion = new TrimRegionCommand("Remove Right", - TrimRegionCommand.TRIM_RIGHT, seqs, column, - viewport.getAlignment(), viewport.getColumnSelection(), - viewport.getSelectionGroup()); + trimRegion = new TrimRegionCommand("Remove Right", false, seqs, + column, viewport.getAlignment()); } statusBar.setText(MessageManager.formatMessage( @@ -2966,6 +2966,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { viewport.showAllHiddenColumns(); repaint(); + viewport.sendSelection(); } @Override @@ -3056,6 +3057,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, public void hideAllButSelection_actionPerformed(ActionEvent e) { toggleHiddenRegions(false, false); + viewport.sendSelection(); } /* @@ -3073,6 +3075,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, viewport.hideAllSelectedSeqs(); viewport.hideSelectedColumns(); alignPanel.paintAlignment(true); + viewport.sendSelection(); } /* @@ -3088,6 +3091,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, viewport.showAllHiddenColumns(); viewport.showAllHiddenSeqs(); alignPanel.paintAlignment(true); + viewport.sendSelection(); } @Override @@ -3095,6 +3099,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { viewport.hideSelectedColumns(); alignPanel.paintAlignment(true); + viewport.sendSelection(); } @Override @@ -3496,6 +3501,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param cs * DOCUMENT ME! */ + @Override public void changeColour(ColourSchemeI cs) { // TODO: pull up to controller method @@ -3515,6 +3521,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel, cs, "Background")); } + if (cs instanceof TCoffeeColourScheme) + { + tcoffeeColour.setEnabled(true); + tcoffeeColour.setSelected(true); + } } viewport.setGlobalColourScheme(cs); @@ -5525,8 +5536,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, @Override public void run() { + boolean isNuclueotide = alignPanel.alignFrame + .getViewport().getAlignment() + .isNucleotide(); new jalview.ws.DBRefFetcher(alignPanel.av - .getSequenceSelection(), alignPanel.alignFrame) + .getSequenceSelection(), + alignPanel.alignFrame, null, + alignPanel.alignFrame.featureSettings, + isNuclueotide) .fetchDBRefs(false); } }).start(); @@ -5595,9 +5612,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, @Override public void run() { + boolean isNuclueotide = alignPanel.alignFrame + .getViewport().getAlignment() + .isNucleotide(); new jalview.ws.DBRefFetcher(alignPanel.av .getSequenceSelection(), - alignPanel.alignFrame, dassource) + alignPanel.alignFrame, dassource, + alignPanel.alignFrame.featureSettings, + isNuclueotide) .fetchDBRefs(false); } }).start(); @@ -5631,9 +5653,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, @Override public void run() { + boolean isNuclueotide = alignPanel.alignFrame + .getViewport().getAlignment() + .isNucleotide(); new jalview.ws.DBRefFetcher(alignPanel.av .getSequenceSelection(), - alignPanel.alignFrame, dassource) + alignPanel.alignFrame, dassource, + alignPanel.alignFrame.featureSettings, + isNuclueotide) .fetchDBRefs(false); } }).start(); @@ -5682,9 +5709,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, @Override public void run() { + boolean isNuclueotide = alignPanel.alignFrame + .getViewport().getAlignment() + .isNucleotide(); new jalview.ws.DBRefFetcher(alignPanel.av .getSequenceSelection(), - alignPanel.alignFrame, dassrc) + alignPanel.alignFrame, dassrc, + alignPanel.alignFrame.featureSettings, + isNuclueotide) .fetchDBRefs(false); } }).start(); @@ -5749,6 +5781,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, viewport.firePropertyChange("alignment", null, al); } + @Override public void setShowSeqFeatures(boolean b) { showSeqFeatures.setSelected(b);