X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignmentPanel.java;h=a4a38f98fce7e525a23ce6edd9dbe425ad520b45;hb=608832fec5a504b4c56e5837b2b3dfc1993fe734;hp=00f27aaac335738f261495cec9644fc724b1c073;hpb=8f56279671fd43b29887fcb33efb52795287342c;p=jalview.git diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java index 00f27aa..a4a38f9 100755 --- a/src/jalview/gui/AlignmentPanel.java +++ b/src/jalview/gui/AlignmentPanel.java @@ -92,11 +92,8 @@ public class AlignmentPanel extends GAlignmentPanel setScrollValues(0, 0); - annotationPanel.adjustPanelHeight(); - annotationSpaceFillerHolder.setPreferredSize(annotationPanel. - getPreferredSize()); - annotationScroller.setPreferredSize(annotationPanel. - getPreferredSize()); + adjustAnnotationHeight(); + setAnnotationVisible(av.getShowAnnotation()); hscroll.addAdjustmentListener(this); @@ -116,8 +113,7 @@ public class AlignmentPanel extends GAlignmentPanel switch (evt.getKeyCode()) { case 27: // escape key - av.setSelectionGroup(null); - repaint(); + alignFrame.deselectAllSequenceMenuItem_actionPerformed(null); break; @@ -161,18 +157,14 @@ public class AlignmentPanel extends GAlignmentPanel break; case KeyEvent.VK_DELETE: - if(av.cursorMode) - { - seqPanel.deleteGapAtCursor(evt.isControlDown() || evt.isShiftDown()); - } - break; - case KeyEvent.VK_BACK_SPACE: if(!av.cursorMode) { alignFrame.cut_actionPerformed(null); - seqPanel.seqCanvas.repaint(); } + else + seqPanel.deleteGapAtCursor(evt.isControlDown() || evt.isShiftDown()); + break; case KeyEvent.VK_S: @@ -182,7 +174,7 @@ public class AlignmentPanel extends GAlignmentPanel } break; case KeyEvent.VK_C: - if(av.cursorMode) + if(av.cursorMode && !evt.isControlDown()) { seqPanel.setCursorColumn(); } @@ -243,6 +235,38 @@ public class AlignmentPanel extends GAlignmentPanel ex.printStackTrace(); } break; + case KeyEvent.VK_H: + { + boolean toggleSeqs = !evt.isControlDown(); + boolean toggleCols = !evt.isShiftDown(); + + boolean hide = false; + + SequenceGroup sg = av.getSelectionGroup(); + if(toggleSeqs) + { + if(sg != null && sg.getSize(false) != av.alignment.getHeight()) + { + alignFrame.hideSelSequences_actionPerformed(null); + hide = true; + } + else if (!(toggleCols && av.colSel.getSelected().size() > 0)) + alignFrame.showAllSeqs_actionPerformed(null); + } + + if (toggleCols) + { + if(av.colSel.getSelected().size() > 0) + { + alignFrame.hideSelColumns_actionPerformed(null); + if(!toggleSeqs) + av.selectionGroup = sg; + } + else if(!hide) + alignFrame.showAllColumns_actionPerformed(null); + } + break; + } } } @@ -371,16 +395,21 @@ public class AlignmentPanel extends GAlignmentPanel } else { - int cwidth = seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel.seqCanvas.getWidth()); - if( start(av.getStartRes()+cwidth) ) - { - vscroll.setValue(start / cwidth); - av.startRes = vscroll.getValue() * cwidth; - } + scrollToWrappedVisible(start); } } } + void scrollToWrappedVisible(int res) + { + int cwidth = seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel.seqCanvas.getWidth()); + if( res<=av.getStartRes() || res>=(av.getStartRes()+cwidth) ) + { + vscroll.setValue(res / cwidth); + av.startRes = vscroll.getValue() * cwidth; + } + } + /** * DOCUMENT ME! * @@ -416,6 +445,37 @@ public class AlignmentPanel extends GAlignmentPanel repaint(); } + public void adjustAnnotationHeight() + { + javax.swing.SwingUtilities.invokeLater(new Runnable() + { + public void run() + { + while(alignFrame.getHeight()==0) + { + Thread.yield(); + } + + int height = annotationPanel.adjustPanelHeight(); + + if (height > alignFrame.getHeight() / 2) + { + height = alignFrame.getHeight() / 2; + } + + annotationScroller.setPreferredSize( + new Dimension(annotationScroller.getWidth(), + height)); + + annotationSpaceFillerHolder.setPreferredSize(new Dimension( + annotationSpaceFillerHolder.getWidth(), + height)); + + annotationPanel.repaint(); + } + }); + } + /** * DOCUMENT ME! * @@ -569,6 +629,7 @@ public class AlignmentPanel extends GAlignmentPanel */ public void adjustmentValueChanged(AdjustmentEvent evt) { + int oldX = av.getStartRes(); int oldY = av.getStartSeq(); @@ -586,10 +647,26 @@ public class AlignmentPanel extends GAlignmentPanel if (av.getWrapAlignment()) { - int rowSize = seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel. - seqCanvas.getWidth()); - av.setStartRes(vscroll.getValue() * rowSize); - av.setEndRes( (vscroll.getValue() + 1) * rowSize); + if(offy>-1) + { + int rowSize = seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel. + seqCanvas.getWidth()); + av.setStartRes(offy * rowSize); + av.setEndRes( (offy + 1) * rowSize); + } + else + { + //This is only called if file loaded is a jar file that + //was wrapped when saved and user has wrap alignment true + //as preference setting + SwingUtilities.invokeLater(new Runnable() + { + public void run() + { + setScrollValues(av.getStartRes(), av.getStartSeq()); + } + }); + } } else { @@ -651,8 +728,14 @@ public class AlignmentPanel extends GAlignmentPanel if (av.getWrapAlignment()) { - int max = av.alignment.getWidth() / - seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel.seqCanvas.getWidth()) +1; + int maxwidth = av.alignment.getWidth(); + + if (av.hasHiddenColumns) + maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1; + + int max = maxwidth / + seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel.seqCanvas.getWidth()) + + 1; vscroll.setMaximum(max); @@ -792,7 +875,7 @@ public class AlignmentPanel extends GAlignmentPanel for (int i = startSeq; i < endSeq; i++) { if ( (av.getSelectionGroup() != null) && - av.getSelectionGroup().sequences.contains( + av.getSelectionGroup().getSequences(false).contains( av.getAlignment().getSequenceAt(i))) { currentColor = Color.gray; @@ -871,10 +954,15 @@ public class AlignmentPanel extends GAlignmentPanel int idWidth = calculateIdWidth().width + 4; + int maxwidth = av.alignment.getWidth(); + if (av.hasHiddenColumns) + maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1; + + int resWidth = seqPanel.seqCanvas.getWrappedCanvasWidth(pwidth - idWidth); - int totalHeight = cHeight * (av.alignment.getWidth() / resWidth + 1); + int totalHeight = cHeight * (maxwidth / resWidth + 1); pg.setColor(Color.white); pg.fillRect(0, 0, pwidth, pheight); @@ -939,9 +1027,12 @@ public class AlignmentPanel extends GAlignmentPanel void makeAlignmentImage(int type, File file) { - int height = ( (av.alignment.getHeight() + 1) * av.charHeight) + 30; - int width = idPanel.getWidth() + (av.alignment.getWidth() * av.charWidth); + int maxwidth = av.alignment.getWidth(); + if (av.hasHiddenColumns) + maxwidth = av.getColumnSelection().findColumnPosition(maxwidth); + int height = ( (av.alignment.getHeight() + 1) * av.charHeight) + 30; + int width = idPanel.getWidth() + (maxwidth * av.charWidth); if (idPanel.getWidth() == 0) { width += calculateIdWidth().getWidth() + 4; @@ -950,7 +1041,14 @@ public class AlignmentPanel extends GAlignmentPanel if (av.getWrapAlignment()) { height = getWrappedHeight(); - width = seqPanel.getWidth() + idPanel.getWidth(); + if (System.getProperty("java.awt.headless") != null + && System.getProperty("java.awt.headless").equals("true")) + { + width = alignFrame.getWidth() - 22; + } + else + width = seqPanel.getWidth() + idPanel.getWidth(); + } else if (av.getShowAnnotation()) { @@ -1123,9 +1221,9 @@ public class AlignmentPanel extends GAlignmentPanel if (features[f].getDescription() != null && !features[f].getType().equals(features[f].getDescription())) text.append(" " + features[f].getDescription()); - if (features[f].getStatus() != null && features[f].getStatus().length()>0) + if (features[f].getValue("status") != null ) { - text.append(" (" + features[f].getStatus() + ")"); + text.append(" (" + features[f].getValue("status") + ")"); } } } @@ -1153,9 +1251,19 @@ public class AlignmentPanel extends GAlignmentPanel int getWrappedHeight() { + int seqPanelWidth = seqPanel.seqCanvas.getWidth(); + + //If headless, seqPanel will have 0 width + if (System.getProperty("java.awt.headless") != null + && System.getProperty("java.awt.headless").equals("true")) + { + int idWidth = calculateIdWidth().width + 4; + seqPanelWidth = alignFrame.getWidth() - idWidth; + } int chunkWidth = seqPanel.seqCanvas.getWrappedCanvasWidth( - seqPanel.seqCanvas.getWidth()); + seqPanelWidth + ); int hgap = av.charHeight; if (av.scaleAboveWrapped) @@ -1171,7 +1279,12 @@ public class AlignmentPanel extends GAlignmentPanel + hgap + annotationHeight; - int height = ( (av.alignment.getWidth() / chunkWidth) + 1) * cHeight; + int maxwidth = av.alignment.getWidth(); + if (av.hasHiddenColumns) + maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1; + + + int height = ( (maxwidth / chunkWidth) + 1) * cHeight; return height; }