X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAlignmentPanel.java;h=9bf1a666d14473ab5d127c1b2d39f3703a51429f;hb=ba1f9fee25b87bdac0c535019252b787939a8f80;hp=f8f31b26e7c896e91d68027efb03e5cef78529f0;hpb=e54df488cd82761bfb0e9372aeae2acc5a1324d7;p=jalview.git diff --git a/src/jalview/appletgui/AlignmentPanel.java b/src/jalview/appletgui/AlignmentPanel.java index f8f31b2..9bf1a66 100644 --- a/src/jalview/appletgui/AlignmentPanel.java +++ b/src/jalview/appletgui/AlignmentPanel.java @@ -46,8 +46,9 @@ import java.awt.event.ComponentEvent; import java.beans.PropertyChangeEvent; import java.util.List; -public class AlignmentPanel extends Panel implements AdjustmentListener, - AlignmentViewPanel, ViewportListenerI +@SuppressWarnings("serial") +public class AlignmentPanel extends Panel + implements AdjustmentListener, AlignmentViewPanel, ViewportListenerI { public AlignViewport av; @@ -73,23 +74,6 @@ public class AlignmentPanel extends Panel implements AdjustmentListener, // this value is set false when selection area being dragged boolean fastPaint = true; - @Override - public void finalize() throws Throwable - { - alignFrame = null; - av = null; - vpRanges = null; - seqPanel = null; - seqPanelHolder = null; - sequenceHolderPanel = null; - scalePanel = null; - scalePanelHolder = null; - annotationPanel = null; - annotationPanelHolder = null; - annotationSpaceFillerHolder = null; - super.finalize(); - } - public AlignmentPanel(AlignFrame af, final AlignViewport av) { try @@ -234,10 +218,10 @@ public class AlignmentPanel extends Panel implements AdjustmentListener, idPanel.idCanvas.image = null; FontMetrics fm = getFontMetrics(av.getFont()); - scalePanel.setSize(new Dimension(10, av.getCharHeight() - + fm.getDescent())); - idwidthAdjuster.setSize(new Dimension(10, av.getCharHeight() - + fm.getDescent())); + scalePanel.setSize( + new Dimension(10, av.getCharHeight() + fm.getDescent())); + idwidthAdjuster.setSize( + new Dimension(10, av.getCharHeight() + fm.getDescent())); av.updateSequenceIdColours(); annotationPanel.image = null; int ap = annotationPanel.adjustPanelHeight(false); @@ -358,11 +342,10 @@ public class AlignmentPanel extends Panel implements AdjustmentListener, * @return false if results were not found */ public boolean scrollToPosition(SearchResultsI results, - int verticalOffset, - boolean redrawOverview, boolean centre) + int verticalOffset, boolean redrawOverview, boolean centre) { // do we need to scroll the panel? - if (results != null && results.getSize() > 0) + if (results != null && results.getCount() > 0) { AlignmentI alignment = av.getAlignment(); int seqIndex = alignment.findIndex(results); @@ -380,8 +363,8 @@ public class AlignmentPanel extends Panel implements AdjustmentListener, { if (JalviewLite.debug) {// DEBUG - System.out - .println("DEBUG: scroll didn't happen - results not within alignment : " + jalview.bin.Console.outPrintln( + "DEBUG: scroll didn't happen - results not within alignment : " + seq.getStart() + "," + seq.getEnd()); } return false; @@ -390,7 +373,7 @@ public class AlignmentPanel extends Panel implements AdjustmentListener, { // DEBUG /* - * System.out.println("DEBUG: scroll: start=" + r[0] + + * jalview.bin.Console.outPrintln("DEBUG: scroll: start=" + r[0] + * " av.getStartRes()=" + av.getStartRes() + " end=" + r[1] + * " seq.end=" + seq.getEnd() + " av.getEndRes()=" + av.getEndRes() + * " hextent=" + hextent); @@ -405,7 +388,8 @@ public class AlignmentPanel extends Panel implements AdjustmentListener, */ if (centre) { - int offset = (vpRanges.getEndRes() - vpRanges.getStartRes() + 1) / 2 - 1; + int offset = (vpRanges.getEndRes() - vpRanges.getStartRes() + 1) / 2 + - 1; start = Math.max(start - offset, 0); end = end + offset - 1; // end = Math.min(end + offset, seq.getEnd() - 1); @@ -432,14 +416,14 @@ public class AlignmentPanel extends Panel implements AdjustmentListener, public boolean scrollTo(int ostart, int end, int seqIndex, boolean scrollToNearest, boolean redrawOverview) { - int startv, endv, starts, ends, width; + int startv, endv, starts, ends;// , width; int start = -1; if (av.hasHiddenColumns()) { AlignmentI al = av.getAlignment(); - start = al.getHiddenColumns().findColumnPosition(ostart); - end = al.getHiddenColumns().findColumnPosition(end); + start = al.getHiddenColumns().absoluteToVisibleColumn(ostart); + end = al.getHiddenColumns().absoluteToVisibleColumn(end); if (start == end) { if (!scrollToNearest && !al.getHiddenColumns().isVisible(ostart)) @@ -518,8 +502,8 @@ public class AlignmentPanel extends Panel implements AdjustmentListener, /* * Scroll down to make end of search results visible */ - setScrollValues(vpRanges.getStartRes(), starts + seqIndex - ends - + 1); + setScrollValues(vpRanges.getStartRes(), + starts + seqIndex - ends + 1); } /* * Else results are already visible - no need to scroll @@ -530,7 +514,7 @@ public class AlignmentPanel extends Panel implements AdjustmentListener, vpRanges.scrollToWrappedVisible(start); } - paintAlignment(redrawOverview); + paintAlignment(redrawOverview, false); return true; } @@ -571,15 +555,15 @@ public class AlignmentPanel extends Panel implements AdjustmentListener, // this is called after loading new annotation onto alignment if (alignFrame.getSize().height == 0) { - System.out - .println("adjustAnnotationHeight frame size zero NEEDS FIXING"); + jalview.bin.Console.outPrintln( + "adjustAnnotationHeight frame size zero NEEDS FIXING"); } fontChanged(); validateAnnotationDimensions(true); apvscroll.addNotify(); hscroll.addNotify(); validate(); - paintAlignment(true); + paintAlignment(true, false); } /** @@ -605,8 +589,8 @@ public class AlignmentPanel extends Panel implements AdjustmentListener, */ if (annotationHeight + alignmentHeight > availableHeight) { - annotationHeight = Math.min(annotationHeight, availableHeight - 2 - * rowHeight); + annotationHeight = Math.min(annotationHeight, + availableHeight - 2 * rowHeight); } } else @@ -623,13 +607,13 @@ public class AlignmentPanel extends Panel implements AdjustmentListener, annotationPanel.setSize(new Dimension(d.width, annotationHeight)); annotationPanelHolder.setSize(new Dimension(d.width, annotationHeight)); // seqPanelHolder.setSize(d.width, seqandannot - height); - seqPanel.seqCanvas - .setSize(d.width, seqPanel.seqCanvas.getSize().height); + seqPanel.seqCanvas.setSize(d.width, + seqPanel.seqCanvas.getSize().height); Dimension e = idPanel.getSize(); alabels.setSize(new Dimension(e.width, annotationHeight)); - annotationSpaceFillerHolder.setSize(new Dimension(e.width, - annotationHeight)); + annotationSpaceFillerHolder + .setSize(new Dimension(e.width, annotationHeight)); int s = apvscroll.getValue(); if (s > mheight - annotationHeight) @@ -643,7 +627,7 @@ public class AlignmentPanel extends Panel implements AdjustmentListener, public void setWrapAlignment(boolean wrap) { - vpRanges.setStartSeq(0); + vpRanges.setStartEndSeq(0, vpRanges.getVisibleAlignmentHeight()); vpRanges.setStartRes(0); scalePanelHolder.setVisible(!wrap); @@ -686,14 +670,9 @@ public class AlignmentPanel extends Panel implements AdjustmentListener, } else { - int width = av.getAlignment().getWidth(); + int width = av.getAlignment().getVisibleWidth(); int height = av.getAlignment().getHeight(); - if (av.hasHiddenColumns()) - { - width = av.getAlignment().getHiddenColumns() - .findColumnPosition(width); - } if (x < 0) { x = 0; @@ -714,7 +693,8 @@ public class AlignmentPanel extends Panel implements AdjustmentListener, if ((hextent + x) > width) { - System.err.println("hextent was " + hextent + " and x was " + x); + jalview.bin.Console + .errPrintln("hextent was " + hextent + " and x was " + x); x = width - hextent; } @@ -731,7 +711,7 @@ public class AlignmentPanel extends Panel implements AdjustmentListener, if (x < 0) { - System.err.println("x was " + x); + jalview.bin.Console.errPrintln("x was " + x); x = 0; } @@ -817,14 +797,14 @@ public class AlignmentPanel extends Panel implements AdjustmentListener, { return; } - else if (newY > -1) + if (newY > -1) { /* * limit page up/down to one width's worth of positions */ int rowSize = vpRanges.getViewportWidth(); int newX = newY > oldY ? oldX + rowSize : oldX - rowSize; - vpRanges.setViewportStartAndWidth(newX, rowSize); + vpRanges.setViewportStartAndWidth(Math.max(0, newX), rowSize); } } else @@ -930,7 +910,8 @@ public class AlignmentPanel extends Panel implements AdjustmentListener, * Repaint the alignment and annotations, and, optionally, any overview window */ @Override - public void paintAlignment(boolean updateOverview) + public void paintAlignment(boolean updateOverview, + boolean updateStructures) { final AnnotationSorter sorter = new AnnotationSorter(getAlignment(), av.isShowAutocalculatedAbove()); @@ -938,13 +919,14 @@ public class AlignmentPanel extends Panel implements AdjustmentListener, av.getSortAnnotationsBy()); repaint(); - if (updateOverview) + if (updateStructures) { - // TODO: determine if this paintAlignment changed structure colours jalview.structure.StructureSelectionManager .getStructureSelectionManager(av.applet) .sequenceColoursChanged(this); - + } + if (updateOverview) + { if (overviewPanel != null) { overviewPanel.updateOverviewImage(); @@ -1130,7 +1112,7 @@ public class AlignmentPanel extends Panel implements AdjustmentListener, public void raiseOOMWarning(String string, OutOfMemoryError error) { // TODO: JAL-960 - System.err.println("Out of memory whilst '" + string + "'"); + jalview.bin.Console.errPrintln("Out of memory whilst '" + string + "'"); error.printStackTrace(); } @@ -1156,7 +1138,7 @@ public class AlignmentPanel extends Panel implements AdjustmentListener, @Override /** - * Property change event fired when a change is made to the viewport ranges + * Property change event fired when a change is made to the viewport ranges * object associated with this alignment panel's viewport */ public void propertyChange(PropertyChangeEvent evt)