X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAlignmentPanel.java;h=0307a96f9e3120fe08292b495193ee5ebec85fa9;hb=07c1edb779cfa11d19ea6e5dc731333e5dfd2250;hp=0e9a0d8ff14cdda2fafbe0cdeb899a020e849e9a;hpb=59183747dbffe3ab6b141c5440d2f70799ae360b;p=jalview.git diff --git a/src/jalview/appletgui/AlignmentPanel.java b/src/jalview/appletgui/AlignmentPanel.java index 0e9a0d8..0307a96 100755 --- a/src/jalview/appletgui/AlignmentPanel.java +++ b/src/jalview/appletgui/AlignmentPanel.java @@ -1,6 +1,6 @@ /* * Jalview - A Sequence Alignment Editor and Viewer - * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License @@ -40,7 +40,7 @@ public class AlignmentPanel extends Panel implements AdjustmentListener // this value is set false when selection area being dragged boolean fastPaint = true; - boolean MAC = false; + public AlignmentPanel(AlignFrame af, final AlignViewport av) { @@ -53,8 +53,6 @@ public class AlignmentPanel extends Panel implements AdjustmentListener e.printStackTrace(); } - if(System.getProperty("os.name").startsWith("Mac")) - MAC = true; alignFrame = af; this.av = av; @@ -63,13 +61,15 @@ public class AlignmentPanel extends Panel implements AdjustmentListener scalePanel = new ScalePanel(av, this); idwidthAdjuster = new IdwidthAdjuster(this); annotationPanel = new AnnotationPanel(this); + + sequenceHolderPanel.add(annotationPanel, BorderLayout.SOUTH); + alabels = new AnnotationLabels(this); setAnnotationVisible(av.showAnnotation); idPanelHolder.add(idPanel, BorderLayout.CENTER); idSpaceFillerPanel1.add(idwidthAdjuster, BorderLayout.CENTER); - annotationScroller.add(annotationPanel); annotationSpaceFillerHolder.add(alabels, BorderLayout.CENTER); scalePanelHolder.add(scalePanel, BorderLayout.CENTER); seqPanelHolder.add(seqPanel, BorderLayout.CENTER); @@ -93,26 +93,54 @@ public class AlignmentPanel extends Panel implements AdjustmentListener idPanel.idCanvas.setSize(d); hscrollFillerPanel.setSize(d.width, annotationPanel.getSize().height); - annotationScroller.setSize(annotationPanel.getSize()); idPanel.idCanvas.setSize(d.width, seqPanel.seqCanvas.getSize().height); annotationSpaceFillerHolder.setSize(d.width, annotationPanel.getSize().height); alabels.setSize(d.width, annotationPanel.getSize().height); + final AlignmentPanel ap = this; + av.addPropertyChangeListener(new java.beans.PropertyChangeListener() + { + public void propertyChange(java.beans.PropertyChangeEvent evt) + { + if (evt.getPropertyName().equals("alignment")) + { + PaintRefresher.Refresh(ap, + av.getSequenceSetId(), + true, + true); + alignmentChanged(); + } + } + }); + } + public void alignmentChanged() + { + av.alignmentChanged(this); + + if (overviewPanel != null) + overviewPanel.updateOverviewImage(); + + alignFrame.updateEditMenuBar(); + + repaint(); + } + public void fontChanged() { // set idCanvas bufferedImage to null // to prevent drawing old image - idPanel.idCanvas.image =null; + idPanel.idCanvas.image = null; FontMetrics fm = getFontMetrics(av.getFont()); scalePanel.setSize(new Dimension(10, av.charHeight + fm.getDescent())); idwidthAdjuster.setSize(new Dimension(10, av.charHeight + fm.getDescent())); + annotationPanel.image = null; int ap = annotationPanel.adjustPanelHeight(); annotationPanel.repaint(); Dimension d = calculateIdWidth(); @@ -138,16 +166,14 @@ public class AlignmentPanel extends Panel implements AdjustmentListener Dimension calculateIdWidth() { - Frame frame = new Frame(); - frame.addNotify(); - Graphics g = frame.getGraphics(); - if (g == null) + if (av.nullFrame == null) { - Frame f = new Frame(); - f.addNotify(); - g = f.getGraphics(); + av.nullFrame = new Frame(); + av.nullFrame.addNotify(); } + Graphics g = av.nullFrame.getGraphics(); + FontMetrics fm = g.getFontMetrics(av.font); AlignmentI al = av.getAlignment(); @@ -170,7 +196,7 @@ public class AlignmentPanel extends Panel implements AdjustmentListener i = 0; if (al.getAlignmentAnnotation() != null) { - fm = g.getFontMetrics(frame.getFont()); + fm = g.getFontMetrics(av.nullFrame.getFont()); while (i < al.getAlignmentAnnotation().length) { String label = al.getAlignmentAnnotation()[i].label; @@ -185,54 +211,58 @@ public class AlignmentPanel extends Panel implements AdjustmentListener return new Dimension(idWidth, idPanel.idCanvas.getSize().height); } - public void highlightSearchResults(int[] results) + public void highlightSearchResults(SearchResults results) { seqPanel.seqCanvas.highlightSearchResults(results); - // do we need to scroll the panel? + // do we need to scroll the panel? if (results != null) { - SequenceI seq = av.alignment.getSequenceAt(results[0]); - int start = seq.findIndex(results[1]) - 1; - int end = seq.findIndex(results[2]) - 1; + SequenceI seq = results.getResultSequence(0); + int seqIndex = av.alignment.findIndex(seq); + int start = seq.findIndex(results.getResultStart(0)) - 1; + int end = seq.findIndex(results.getResultEnd(0)) - 1; - if(!av.wrapAlignment) - { - if ( (av.getStartRes() > start) || (av.getEndRes() < end) || - ( (av.getStartSeq() > results[0]) || - (av.getEndSeq() < results[0]))) + if(!av.wrapAlignment) { - int newy = results[0]; - if(start > av.alignment.getWidth() - hextent) + if ( (av.getStartRes() > end) || (av.getEndRes() < start) || + ( (av.getStartSeq() > seqIndex) || (av.getEndSeq() < seqIndex))) { - start = av.alignment.getWidth() - hextent; - if(start<0) - start = 0; + if (start > av.alignment.getWidth() - hextent) + { + start = av.alignment.getWidth() - hextent; + if (start < 0) + start = 0; + } + if (seqIndex > av.alignment.getHeight() - vextent) + { + seqIndex = av.alignment.getHeight() - vextent; + if (seqIndex < 0) + seqIndex = 0; + } + setScrollValues(start, seqIndex); } - if(newy > av.alignment.getHeight() - vextent) - { - newy = av.alignment.getHeight() - vextent; - if(newy<0) - newy = 0; - } - setScrollValues(start, newy); } - } - else - { - int cwidth = seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel.seqCanvas.getSize().width); - if( start(av.getStartRes()+cwidth) ) + else { - - vscroll.setValue(start / cwidth); - av.startRes = vscroll.getValue() * cwidth; + scrollToWrappedVisible(start); } - } } repaint(); } + void scrollToWrappedVisible(int res) + { + int cwidth = seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel.seqCanvas.getSize().width); + if (res <= av.getStartRes() || res >= (av.getStartRes() + cwidth)) + { + vscroll.setValue(res / cwidth); + av.startRes = vscroll.getValue() * cwidth; + } + } + + public OverviewPanel getOverviewPanel() { return overviewPanel; @@ -248,7 +278,7 @@ public class AlignmentPanel extends Panel implements AdjustmentListener if (!av.wrapAlignment) { annotationSpaceFillerHolder.setVisible(b); - annotationScroller.setVisible(b); + annotationPanel.setVisible(b); } validate(); repaint(); @@ -265,12 +295,12 @@ public class AlignmentPanel extends Panel implements AdjustmentListener if (wrap) { - annotationScroller.setVisible(false); + annotationPanel.setVisible(false); annotationSpaceFillerHolder.setVisible(false); } else if (av.showAnnotation) { - annotationScroller.setVisible(true); + annotationPanel.setVisible(true); annotationSpaceFillerHolder.setVisible(true); } @@ -297,8 +327,7 @@ public class AlignmentPanel extends Panel implements AdjustmentListener { return false; } - fastPaint = false; - vscroll.setValue(vscroll.getValue() - 1); + setScrollValues(hscroll.getValue(), vscroll.getValue()-1); } else { @@ -306,24 +335,22 @@ public class AlignmentPanel extends Panel implements AdjustmentListener { return false; } - fastPaint = false; - vscroll.setValue(vscroll.getValue() + 1); + setScrollValues(hscroll.getValue(), vscroll.getValue()+1); } - fastPaint = true; + + repaint(); return true; } public boolean scrollRight(boolean right) { - - if (right) + if (!right) { if (hscroll.getValue() < 1) { return false; } - fastPaint = false; - hscroll.setValue(hscroll.getValue() - 1); + setScrollValues(hscroll.getValue()-1, vscroll.getValue()); } else { @@ -331,40 +358,47 @@ public class AlignmentPanel extends Panel implements AdjustmentListener { return false; } - fastPaint = false; - hscroll.setValue(hscroll.getValue() + 1); + setScrollValues(hscroll.getValue()+1, vscroll.getValue()); } - fastPaint = true; + + repaint(); return true; } public void setScrollValues(int x, int y) { + int width = av.alignment.getWidth(); + int height = av.alignment.getHeight(); + + if(av.hasHiddenColumns) + width = av.getColumnSelection().findColumnPosition(width); av.setStartRes(x); av.setStartSeq(y); - av.setEndRes(x + seqPanel.seqCanvas.getSize().width / av.getCharWidth() - 1); + + av.setEndRes( (x + (seqPanel.seqCanvas.getSize().width / av.charWidth)) -1); hextent = seqPanel.seqCanvas.getSize().width / av.charWidth; vextent = seqPanel.seqCanvas.getSize().height / av.charHeight; - if (hextent > av.alignment.getWidth()) + if (hextent > width) { - hextent = av.alignment.getWidth(); + hextent = width; } - if (vextent > av.alignment.getHeight()) + + if (vextent > height) { - vextent = av.alignment.getHeight(); + vextent = height; } - if (hextent + x > av.getAlignment().getWidth()) + if ( (hextent + x) > width) { - x = av.getAlignment().getWidth() - hextent; + x = width - hextent; } - if (vextent + y > av.getAlignment().getHeight()) + if ( (vextent + y) > height) { - y = av.getAlignment().getHeight() - vextent; + y = height - vextent; } if (y < 0) @@ -387,6 +421,9 @@ public class AlignmentPanel extends Panel implements AdjustmentListener hscroll.setValues(x, hextent, 0, av.getAlignment().getWidth()); vscroll.setValues(y, vextent, 0, av.getAlignment().getHeight()); + if(overviewPanel!=null) + overviewPanel.setBoxPosition(); + } public void adjustmentValueChanged(AdjustmentEvent evt) @@ -394,6 +431,7 @@ public class AlignmentPanel extends Panel implements AdjustmentListener int oldX = av.getStartRes(); int oldY = av.getStartSeq(); + if (evt==null || evt.getSource() == hscroll) { int x = hscroll.getValue(); @@ -402,6 +440,7 @@ public class AlignmentPanel extends Panel implements AdjustmentListener 1); } + if (evt==null || evt.getSource() == vscroll) { int offy = vscroll.getValue(); @@ -428,16 +467,18 @@ public class AlignmentPanel extends Panel implements AdjustmentListener int scrollX = av.startRes - oldX; int scrollY = av.startSeq - oldY; - if (av.getWrapAlignment() || !fastPaint || MAC) + if (av.getWrapAlignment() || !fastPaint || av.MAC) { repaint(); } - else if(!seqPanel.seqCanvas.fastPaint) + else { // Make sure we're not trying to draw a panel // larger than the visible window if(scrollX>av.endRes-av.startRes) - scrollX = av.endRes-av.startRes; + { + scrollX = av.endRes - av.startRes; + } else if(scrollX0) + { + int max = maxwidth / canvasWidth; + vscroll.setMaximum(max); + vscroll.setUnitIncrement(1); + vscroll.setVisibleAmount(1); + } } else { @@ -514,7 +565,6 @@ public class AlignmentPanel extends Panel implements AdjustmentListener BorderLayout borderLayout10 = new BorderLayout(); protected Panel hscrollFillerPanel = new Panel(); BorderLayout borderLayout11 = new BorderLayout(); - public Panel annotationScroller = new Panel(); BorderLayout borderLayout4 = new BorderLayout(); BorderLayout borderLayout2 = new BorderLayout(); @@ -549,11 +599,9 @@ public class AlignmentPanel extends Panel implements AdjustmentListener // this.setPreferredSize(new Dimension(220, 166)); seqPanelHolder.setBackground(Color.white); idPanelHolder.setBackground(Color.white); - annotationScroller.setLayout(borderLayout2); sequenceHolderPanel.add(scalePanelHolder, BorderLayout.NORTH); sequenceHolderPanel.add(seqPanelHolder, BorderLayout.CENTER); seqPanelHolder.add(vscroll, BorderLayout.EAST); - sequenceHolderPanel.add(annotationScroller, BorderLayout.SOUTH); // Panel3.add(secondaryPanelHolder, BorderLayout.SOUTH); this.add(idPanelHolder, BorderLayout.WEST);