X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAlignmentPanel.java;h=224b9662359b356a1439eab748683eede64c58e5;hb=797df64fa2a0a30773d0f48f5494d4155e5a8be3;hp=b27554756c1a9d554c307d1358dd61f17727b1c3;hpb=8a1e2a4d0ad11b139bbdb27010a0c00d12973d6a;p=jalview.git diff --git a/src/jalview/appletgui/AlignmentPanel.java b/src/jalview/appletgui/AlignmentPanel.java old mode 100755 new mode 100644 index b275547..224b966 --- 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, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle * * This file is part of Jalview. * @@ -24,6 +24,7 @@ import java.util.Vector; import jalview.api.AlignmentViewPanel; import jalview.datamodel.*; +import jalview.structure.StructureSelectionManager; public class AlignmentPanel extends Panel implements AdjustmentListener, AlignmentViewPanel { @@ -48,7 +49,19 @@ public class AlignmentPanel extends Panel implements AdjustmentListener, Alignme // 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 @@ -92,8 +105,12 @@ public class AlignmentPanel extends Panel implements AdjustmentListener, Alignme public void componentResized(ComponentEvent evt) { setScrollValues(av.getStartRes(), av.getStartSeq()); + if (getSize().height>0 && annotationPanelHolder.getSize().height>0) { + validateAnnotationDimensions(false); + } repaint(); } + }); Dimension d = calculateIdWidth(); @@ -160,6 +177,7 @@ public class AlignmentPanel extends Panel implements AdjustmentListener, Alignme 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); @@ -264,6 +282,7 @@ public class AlignmentPanel extends Panel implements AdjustmentListener, Alignme public boolean scrollToPosition(SearchResults results, boolean redrawOverview) { + // do we need to scroll the panel? if (results != null && results.getSize() > 0) { @@ -283,10 +302,11 @@ public class AlignmentPanel extends Panel implements AdjustmentListener, Alignme } if (av.applet.debug) { // DEBUG - System.out.println("DEBUG: scroll didn't happen: start=" + r[0] + /*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]; @@ -298,21 +318,57 @@ public class AlignmentPanel extends Panel implements AdjustmentListener, Alignme { 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))) @@ -334,14 +390,14 @@ public class AlignmentPanel extends Panel implements AdjustmentListener, Alignme seqIndex = 0; } } + // System.out.println("trying to scroll to: "+start+" "+seqIndex); setScrollValues(start, seqIndex); - } + }/**/ } else { scrollToWrappedVisible(start); } - } if (redrawOverview && overviewPanel != null) { overviewPanel.setBoxPosition(); @@ -381,7 +437,75 @@ public class AlignmentPanel extends Panel implements AdjustmentListener, Alignme 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; @@ -471,9 +595,7 @@ public class AlignmentPanel extends Panel implements AdjustmentListener, Alignme { 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; @@ -490,6 +612,8 @@ public class AlignmentPanel extends Panel implements AdjustmentListener, Alignme if ((hextent + x) > width) { + System.err.println("hextent was "+hextent+" and x was "+x); + x = width - hextent; } @@ -505,6 +629,7 @@ public class AlignmentPanel extends Panel implements AdjustmentListener, Alignme if (x < 0) { + System.err.println("x was "+x); x = 0; } @@ -517,6 +642,9 @@ public class AlignmentPanel extends Panel implements AdjustmentListener, Alignme } 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); @@ -524,6 +652,8 @@ public class AlignmentPanel extends Panel implements AdjustmentListener, Alignme { overviewPanel.setBoxPosition(); } + sendViewPosition(); + } @@ -601,8 +731,13 @@ public class AlignmentPanel extends Panel implements AdjustmentListener, Alignme 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) { @@ -611,7 +746,7 @@ public class AlignmentPanel extends Panel implements AdjustmentListener, Alignme if (updateOverview) { jalview.structure.StructureSelectionManager - .getStructureSelectionManager().sequenceColoursChanged(this); + .getStructureSelectionManager(av.applet).sequenceColoursChanged(this); if (overviewPanel != null) { @@ -834,67 +969,15 @@ public class AlignmentPanel extends Panel implements AdjustmentListener, Alignme 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(); - validateAnnotationDimensions(true); - apvscroll.addNotify(); - hscroll.addNotify(); - validate(); - addNotify(); - repaint(); - } - /** - * calculate the annotation dimensions and refresh slider values accordingly. - * need to do repaints/notifys afterwards. - */ - protected void validateAnnotationDimensions(boolean adjustPanelHeight) { - int height = annotationPanel.calcPanelHeight(); - if (hscroll.isVisible()) - { - height += hscroll.getPreferredSize().height; - } - int mheight = height; - // sets initial preferred height - if ((height+40) > getSize().height / 2) - { - height = getSize().height / 2; - } - if (!adjustPanelHeight) - { - // maintain same window layout whilst updating sliders - height=seqPanelHolder.getSize().height; - } - Dimension d=seqPanelHolder.getSize(),e=idPanel.getSize(); - annotationPanel.setSize(new Dimension(d.width,height)); - alabels.setSize(e.width,height); - annotationSpaceFillerHolder.setSize(new Dimension(e.width, height)); - annotationPanelHolder.setSize(new Dimension(d.width, height)); - seqPanelHolder.setSize(d.width,d.height-height); - int s=apvscroll.getValue(); - if (s>mheight-height) - { - s = 0; - } - apvscroll.setValues(apvscroll.getValue(), height, 0, mheight); - annotationPanel.setScrollOffset(apvscroll.getValue()); - alabels.setScrollOffset(apvscroll.getValue()); - } - @Override public AlignmentI getAlignment() { return av.alignment; } + @Override + public StructureSelectionManager getStructureSelectionManager() + { + return StructureSelectionManager.getStructureSelectionManager(av.applet); + } }