X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAlignmentPanel.java;h=08d1f850796cf0b2a23ccdcc713593ee33056b10;hb=a45774ee31d9f35d4eff46d54d7deab719afb092;hp=05ecdccf991351bebf81b05b1f1371051f38581d;hpb=dca8d7b5caa5c263b01d7750098da075c892c9f4;p=jalview.git diff --git a/src/jalview/appletgui/AlignmentPanel.java b/src/jalview/appletgui/AlignmentPanel.java old mode 100755 new mode 100644 index 05ecdcc..08d1f85 --- a/src/jalview/appletgui/AlignmentPanel.java +++ b/src/jalview/appletgui/AlignmentPanel.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6) - * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7) + * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle * * This file is part of Jalview. * @@ -22,9 +22,11 @@ import java.awt.event.*; import java.util.Hashtable; import java.util.Vector; +import jalview.api.AlignmentViewPanel; import jalview.datamodel.*; +import jalview.structure.StructureSelectionManager; -public class AlignmentPanel extends Panel implements AdjustmentListener +public class AlignmentPanel extends Panel implements AdjustmentListener, AlignmentViewPanel { public AlignViewport av; @@ -47,7 +49,19 @@ public class AlignmentPanel extends Panel implements AdjustmentListener // this value is set false when selection area being dragged boolean fastPaint = true; - + + public void finalize() { + alignFrame=null; + av=null; + seqPanel=null; + seqPanelHolder=null; + sequenceHolderPanel=null; + scalePanel=null; + scalePanelHolder=null; + annotationPanel=null; + annotationPanelHolder=null; + annotationSpaceFillerHolder=null; + } public AlignmentPanel(AlignFrame af, final AlignViewport av) { try @@ -64,14 +78,9 @@ public class AlignmentPanel extends Panel implements AdjustmentListener idPanel = new IdPanel(av, this); scalePanel = new ScalePanel(av, this); idwidthAdjuster = new IdwidthAdjuster(this); -// annotationScroller = new ScrollPane(); - // annotationScroller.setBackground(Color.white); annotationPanel = new AnnotationPanel(this); annotationPanelHolder.add(annotationPanel, BorderLayout.CENTER); - // annotationScroller.setPreferredSize(new Dimension(10,80)); -// annotationScroller.add(annotationPanel); -// annotationScroller.getInsets().set(0,0,0,0); - + sequenceHolderPanel.add(annotationPanelHolder, BorderLayout.SOUTH); alabels = new AnnotationLabels(this); @@ -83,7 +92,7 @@ public class AlignmentPanel extends Panel implements AdjustmentListener annotationSpaceFillerHolder.add(alabels, BorderLayout.CENTER); scalePanelHolder.add(scalePanel, BorderLayout.CENTER); seqPanelHolder.add(seqPanel, BorderLayout.CENTER); - + fontChanged(); setScrollValues(0, 0); @@ -96,8 +105,12 @@ public class AlignmentPanel extends Panel implements AdjustmentListener public void componentResized(ComponentEvent evt) { setScrollValues(av.getStartRes(), av.getStartSeq()); + if (getSize().height>0 && annotationPanelHolder.getSize().height>0) { + validateAnnotationDimensions(false); + } repaint(); } + }); Dimension d = calculateIdWidth(); @@ -161,13 +174,15 @@ public class AlignmentPanel extends Panel implements AdjustmentListener av.updateSequenceIdColours(); annotationPanel.image = null; int ap = annotationPanel.adjustPanelHeight(false); - annotationPanel.repaint(); Dimension d = calculateIdWidth(); d.setSize(d.width + 4, seqPanel.seqCanvas.getSize().height); alabels.setSize(d.width + 4, ap); + idPanel.idCanvas.setSize(d); hscrollFillerPanel.setSize(d); - + + validateAnnotationDimensions(false); + annotationPanel.repaint(); validate(); repaint(); @@ -181,6 +196,7 @@ public class AlignmentPanel extends Panel implements AdjustmentListener { idPanel.idCanvas.setSize(w, h); idPanelHolder.setSize(w, idPanelHolder.getSize().height); + annotationSpaceFillerHolder.setSize(w,annotationSpaceFillerHolder.getSize().height); alabels.setSize(w, alabels.getSize().height); validate(); } @@ -266,6 +282,7 @@ public class AlignmentPanel extends Panel implements AdjustmentListener public boolean scrollToPosition(SearchResults results, boolean redrawOverview) { + // do we need to scroll the panel? if (results != null && results.getSize() > 0) { @@ -275,11 +292,22 @@ public class AlignmentPanel extends Panel implements AdjustmentListener return false; } SequenceI seq = av.alignment.getSequenceAt(seqIndex); - int[] r = results.getResults(seq, seq.getStart(), seq.getEnd()); + int[] r = results.getResults(seq, 0,av.alignment.getWidth()); if (r == null) { + if (av.applet.debug) {// DEBUG + System.out.println("DEBUG: scroll didn't happen - results not within alignment : "+seq.getStart()+","+seq.getEnd()); + } return false; } + if (av.applet.debug) { + // DEBUG + /*System.out.println("DEBUG: scroll: start=" + r[0] + + " av.getStartRes()=" + av.getStartRes() + " end=" + r[1] + + " seq.end=" + seq.getEnd() + " av.getEndRes()=" + + av.getEndRes() + " hextent=" + hextent); + */ + } int start = r[0]; int end = r[1]; if (start < 0) @@ -290,21 +318,57 @@ public class AlignmentPanel extends Panel implements AdjustmentListener { return false; } - if (av.hasHiddenColumns) + return scrollTo(start, end, seqIndex, false, redrawOverview); + } + return true; + } + public boolean scrollTo(int ostart, int end, int seqIndex, boolean scrollToNearest, boolean redrawOverview) + { + int startv, endv, starts, ends, width; + + int start=-1; + if (av.hasHiddenColumns) + { + start = av.getColumnSelection().findColumnPosition(ostart); + end = av.getColumnSelection().findColumnPosition(end); + if (start == end) { - start = av.getColumnSelection().findColumnPosition(start); - end = av.getColumnSelection().findColumnPosition(end); - if (start == end) + if (!scrollToNearest && !av.colSel.isVisible(ostart)) { - if (!av.colSel.isVisible(r[0])) - { - // don't scroll - position isn't visible - return false; - } + // don't scroll - position isn't visible + return false; } } - if (!av.wrapAlignment) - { + } + else + { + start = ostart; + } + if (!av.wrapAlignment) + { + /* + int spos=av.getStartRes(),sqpos=av.getStartSeq(); + if ((startv = av.getStartRes()) >= start) + { + spos=start-1; +// seqIn +// setScrollValues(start - 1, seqIndex); + } + else if ((endv = av.getEndRes()) <= end) + { +// setScrollValues(spos=startv + 1 + end - endv, seqIndex); + spos=startv + 1 + end - endv; + } + else if ((starts = av.getStartSeq()) > seqIndex) + { + setScrollValues(av.getStartRes(), seqIndex); + } + else if ((ends = av.getEndSeq()) <= seqIndex) + { + setScrollValues(av.getStartRes(), starts + seqIndex - ends + 1); + } + + /* */ if ((av.getStartRes() > end) || (av.getEndRes() < start) || ((av.getStartSeq() > seqIndex) || (av.getEndSeq() < seqIndex))) @@ -316,6 +380,7 @@ public class AlignmentPanel extends Panel implements AdjustmentListener { start = 0; } + } if (seqIndex > av.alignment.getHeight() - vextent) { @@ -325,14 +390,14 @@ public class AlignmentPanel extends Panel implements AdjustmentListener seqIndex = 0; } } + // System.out.println("trying to scroll to: "+start+" "+seqIndex); setScrollValues(start, seqIndex); - } + }/**/ } else { scrollToWrappedVisible(start); } - } if (redrawOverview && overviewPanel != null) { overviewPanel.setBoxPosition(); @@ -367,12 +432,80 @@ public class AlignmentPanel extends Panel implements AdjustmentListener if (!av.wrapAlignment) { annotationSpaceFillerHolder.setVisible(b); - annotationPanel.setVisible(b); + annotationPanelHolder.setVisible(b); } validate(); repaint(); } - + + /** + * automatically adjust annotation panel height for new annotation whilst + * ensuring the alignment is still visible. + */ + public void adjustAnnotationHeight() + { + // TODO: display vertical annotation scrollbar if necessary + // this is called after loading new annotation onto alignment + if (alignFrame.getSize().height == 0) + { + System.out.println("NEEDS FIXING"); + } + fontChanged(); + validateAnnotationDimensions(true); + apvscroll.addNotify(); + hscroll.addNotify(); + validate(); + paintAlignment(true); + } + /** + * calculate the annotation dimensions and refresh slider values accordingly. + * need to do repaints/notifys afterwards. + */ + protected void validateAnnotationDimensions(boolean adjustPanelHeight) { + boolean modified=false; + int height = annotationPanel.calcPanelHeight(); + int minsize=0; + if (hscroll.isVisible()) + { + height += (minsize=hscroll.getPreferredSize().height); + } + if (apvscroll.isVisible()) { + minsize+=apvscroll.getPreferredSize().height; + } + int mheight = height; + Dimension d=sequenceHolderPanel.getSize(),e=idPanel.getSize(); + int seqandannot=d.height-scalePanelHolder.getSize().height; + // sets initial preferred height + if ((height+40) > seqandannot / 2) + { + height = seqandannot / 2; + } + if (!adjustPanelHeight) + { + // maintain same window layout whilst updating sliders + height=annotationPanelHolder.getSize().height; + } + + if (seqandannot-height<5) + { + height = seqandannot; + } + annotationPanel.setSize(new Dimension(d.width,height)); + alabels.setSize(new Dimension(e.width,height)); + annotationSpaceFillerHolder.setSize(new Dimension(e.width, height)); + annotationPanelHolder.setSize(new Dimension(d.width, height)); + seqPanelHolder.setSize(d.width,seqandannot-height); + seqPanel.seqCanvas.setSize(d.width, seqPanel.seqCanvas.getSize().height); + int s=apvscroll.getValue(); + if (s>mheight-height) + { + s = 0; + } + apvscroll.setValues(s, height, 0, mheight); + annotationPanel.setScrollOffset(apvscroll.getValue()); + alabels.setScrollOffset(apvscroll.getValue()); + } + public void setWrapAlignment(boolean wrap) { av.startSeq = 0; @@ -384,12 +517,12 @@ public class AlignmentPanel extends Panel implements AdjustmentListener if (wrap) { - annotationPanel.setVisible(false); + annotationPanelHolder.setVisible(false); annotationSpaceFillerHolder.setVisible(false); } else if (av.showAnnotation) { - annotationPanel.setVisible(true); + annotationPanelHolder.setVisible(true); annotationSpaceFillerHolder.setVisible(true); } @@ -462,13 +595,11 @@ public class AlignmentPanel extends Panel implements AdjustmentListener { width = av.getColumnSelection().findColumnPosition(width); } - - av.setStartRes(x); - av.setEndRes((x + (seqPanel.seqCanvas.getSize().width / av.charWidth)) - 1); + if (x<0) { x = 0; }; hextent = seqPanel.seqCanvas.getSize().width / av.charWidth; vextent = seqPanel.seqCanvas.getSize().height / av.charHeight; - + if (hextent > width) { hextent = width; @@ -481,6 +612,8 @@ public class AlignmentPanel extends Panel implements AdjustmentListener if ((hextent + x) > width) { + System.err.println("hextent was "+hextent+" and x was "+x); + x = width - hextent; } @@ -496,6 +629,7 @@ public class AlignmentPanel extends Panel implements AdjustmentListener if (x < 0) { + System.err.println("x was "+x); x = 0; } @@ -508,6 +642,9 @@ public class AlignmentPanel extends Panel implements AdjustmentListener } av.setEndSeq(endSeq); + av.setStartRes(x); + av.setEndRes((x + (seqPanel.seqCanvas.getSize().width / av.charWidth)) - 1); + hscroll.setValues(x, hextent, 0, width); vscroll.setValues(y, vextent, 0, height); @@ -515,6 +652,8 @@ public class AlignmentPanel extends Panel implements AdjustmentListener { overviewPanel.setBoxPosition(); } + sendViewPosition(); + } @@ -523,14 +662,14 @@ public class AlignmentPanel extends Panel implements AdjustmentListener int oldX = av.getStartRes(); int oldY = av.getStartSeq(); - if (evt == null || evt.getSource()==apvscroll) + if (evt == null || evt.getSource() == apvscroll) { annotationPanel.setScrollOffset(apvscroll.getValue()); alabels.setScrollOffset(apvscroll.getValue()); - //annotationPanel.image=null; - //alabels.image=null; - //alabels.repaint(); - //annotationPanel.repaint(); + // annotationPanel.image=null; + // alabels.image=null; + // alabels.repaint(); + // annotationPanel.repaint(); } if (evt == null || evt.getSource() == hscroll) { @@ -592,8 +731,13 @@ public class AlignmentPanel extends Panel implements AdjustmentListener annotationPanel.fastPaint(av.getStartRes() - oldX); } } + sendViewPosition(); } + private void sendViewPosition() + { + StructureSelectionManager.getStructureSelectionManager(av.applet).sendViewPosition(this, av.startRes, av.endRes, av.startSeq, av.endSeq); + } public void paintAlignment(boolean updateOverview) { @@ -602,7 +746,7 @@ public class AlignmentPanel extends Panel implements AdjustmentListener if (updateOverview) { jalview.structure.StructureSelectionManager - .getStructureSelectionManager().sequenceColoursChanged(this); + .getStructureSelectionManager(av.applet).sequenceColoursChanged(this); if (overviewPanel != null) { @@ -621,12 +765,7 @@ public class AlignmentPanel extends Panel implements AdjustmentListener invalidate(); Dimension d = idPanel.idCanvas.getSize(); idPanel.idCanvas.setSize(d.width, seqPanel.seqCanvas.getSize().height); - annotationPanelHolder.setSize(seqPanel.getSize().width, annotationPanel.getSize().height); - annotationSpaceFillerHolder.setSize(d.width, - annotationPanel.getSize().height); - - alabels.setSize(d.width, annotationPanelHolder.getSize().height); - + if (av.getWrapAlignment()) { int maxwidth = av.alignment.getWidth(); @@ -642,7 +781,7 @@ public class AlignmentPanel extends Panel implements AdjustmentListener if (canvasWidth > 0) { int max = maxwidth / canvasWidth; - vscroll.setMaximum(1+max); + vscroll.setMaximum(1 + max); vscroll.setUnitIncrement(1); vscroll.setVisibleAmount(1); } @@ -699,7 +838,8 @@ public class AlignmentPanel extends Panel implements AdjustmentListener BorderLayout borderLayout2 = new BorderLayout(); Panel annotationPanelHolder = new Panel(); - protected Scrollbar apvscroll=new Scrollbar(); + + protected Scrollbar apvscroll = new Scrollbar(); BorderLayout borderLayout12 = new BorderLayout(); @@ -708,7 +848,7 @@ public class AlignmentPanel extends Panel implements AdjustmentListener // idPanelHolder.setPreferredSize(new Dimension(70, 10)); this.setLayout(borderLayout7); - // sequenceHolderPanel.setPreferredSize(new Dimension(150, 150)); + //sequenceHolderPanel.setPreferredSize(new Dimension(150, 150)); sequenceHolderPanel.setLayout(borderLayout3); seqPanelHolder.setLayout(borderLayout1); scalePanelHolder.setBackground(Color.white); @@ -828,47 +968,16 @@ public class AlignmentPanel extends Panel implements AdjustmentListener oldrfs.clear(); adjustAnnotationHeight(); } - /** - * automatically adjust annotation panel height for new annotation - * whilst ensuring the alignment is still visible. - */ - public void adjustAnnotationHeight() - { - // TODO: display vertical annotation scrollbar if necessary - // this is called after loading new annotation onto alignment - if (alignFrame.getSize().height == 0) - { - System.out.println("NEEDS FIXING"); - } - fontChanged(); - int height = annotationPanel.adjustPanelHeight(); - if (hscroll.isVisible()) - { - height += hscroll.getPreferredSize().height; - } - int mheight=height; - // sets initial preferred height - if (height > alignFrame.getHeight() / 2) - { - height = alignFrame.getHeight() / 2; - } - apvscroll.setValues(apvscroll.getValue(), height, 0, mheight); - annotationPanel.setScrollOffset(apvscroll.getValue()); - alabels.setScrollOffset(apvscroll.getValue()); - apvscroll.addNotify(); - hscroll.addNotify(); - annotationPanelHolder.setSize(new Dimension(annotationPanel - .getSize().width, height)); - - annotationSpaceFillerHolder.setSize(new Dimension( - annotationSpaceFillerHolder.getSize().width - , height)); - - //annotationScroller.validate();// repaint(); - validate(); - addNotify(); - repaint(); + @Override + public AlignmentI getAlignment() + { + return av.alignment; + } + @Override + public StructureSelectionManager getStructureSelectionManager() + { + return StructureSelectionManager.getStructureSelectionManager(av.applet); } }