X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignmentPanel.java;h=395f6b3a253eed1b6524f2e381799abd1a8cf657;hb=d8ca2529b8e334195e29723211fb05e84bac6e03;hp=64250883d7ef0383940a0fa538b767e82baa5da4;hpb=5312252fee162e6bc9bf5ac355930e16f1776c53;p=jalview.git diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java index 6425088..395f6b3 100644 --- a/src/jalview/gui/AlignmentPanel.java +++ b/src/jalview/gui/AlignmentPanel.java @@ -25,6 +25,7 @@ import jalview.api.AlignViewportI; import jalview.api.AlignmentViewPanel; import jalview.bin.Cache; import jalview.datamodel.AlignmentI; +import jalview.datamodel.HiddenColumns; import jalview.datamodel.SearchResultsI; import jalview.datamodel.SequenceFeature; import jalview.datamodel.SequenceGroup; @@ -104,12 +105,14 @@ public class AlignmentPanel extends GAlignmentPanel implements /* * Flag set while scrolling to follow complementary cDNA/protein scroll. When - * true, suppresses invoking the same method recursively. + * false, suppresses invoking the same method recursively. */ - private boolean dontScrollComplement; + private boolean scrollComplementaryPanel = true; private PropertyChangeListener propertyChangeListener; + private CalculationChooser calculationDialog; + /** * Creates a new AlignmentPanel object. * @@ -203,6 +206,11 @@ public class AlignmentPanel extends GAlignmentPanel implements { av.alignmentChanged(this); + if (getCalculationDialog() != null) + { + getCalculationDialog().validateCalcTypes(); + } + alignFrame.updateEditMenuBar(); paintAlignment(true); @@ -401,9 +409,6 @@ public class AlignmentPanel extends GAlignmentPanel implements } int start = r[0]; int end = r[1]; - // DEBUG - // System.err.println(this.av.viewName + " Seq : " + seqIndex - // + " Scroll to " + start + "," + end); /* * To centre results, scroll to positions half the visible width @@ -411,7 +416,8 @@ public class AlignmentPanel extends GAlignmentPanel implements */ 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; } @@ -425,11 +431,12 @@ public class AlignmentPanel extends GAlignmentPanel implements } if (av.hasHiddenColumns()) { - start = av.getColumnSelection().findColumnPosition(start); - end = av.getColumnSelection().findColumnPosition(end); + HiddenColumns hidden = av.getAlignment().getHiddenColumns(); + start = hidden.findColumnPosition(start); + end = hidden.findColumnPosition(end); if (start == end) { - if (!av.getColumnSelection().isVisible(r[0])) + if (!hidden.isVisible(r[0])) { // don't scroll - position isn't visible return false; @@ -442,9 +449,6 @@ public class AlignmentPanel extends GAlignmentPanel implements */ seqIndex = Math.max(0, seqIndex - verticalOffset); - // System.out.println("start=" + start + ", end=" + end + ", startv=" - // + av.getStartRes() + ", endv=" + av.getEndRes() + ", starts=" - // + av.getStartSeq() + ", ends=" + av.getEndSeq()); if (!av.getWrapAlignment()) { if ((startv = vpRanges.getStartRes()) >= start) @@ -452,7 +456,6 @@ public class AlignmentPanel extends GAlignmentPanel implements /* * Scroll left to make start of search results visible */ - // setScrollValues(start - 1, seqIndex); // plus one residue setScrollValues(start, seqIndex); } else if ((endv = vpRanges.getEndRes()) <= end) @@ -460,7 +463,6 @@ public class AlignmentPanel extends GAlignmentPanel implements /* * Scroll right to make end of search results visible */ - // setScrollValues(startv + 1 + end - endv, seqIndex); // plus one setScrollValues(startv + end - endv, seqIndex); } else if ((starts = vpRanges.getStartSeq()) > seqIndex) @@ -659,8 +661,11 @@ public class AlignmentPanel extends GAlignmentPanel implements * visible row to scroll to * */ - public void setScrollValues(int x, int y) + public void setScrollValues(int xpos, int ypos) { + int x = xpos; + int y = ypos; + if (av == null || av.getAlignment() == null) { return; @@ -672,14 +677,13 @@ public class AlignmentPanel extends GAlignmentPanel implements } else { - int width = av.getAlignment().getWidth(); int height = av.getAlignment().getHeight(); if (av.hasHiddenColumns()) { // reset the width to exclude hidden columns - width = av.getColumnSelection().findColumnPosition(width); + width = av.getAlignment().getHiddenColumns().findColumnPosition(width); } hextent = getSeqPanel().seqCanvas.getWidth() / av.getCharWidth(); @@ -722,10 +726,11 @@ public class AlignmentPanel extends GAlignmentPanel implements } /** - * DOCUMENT ME! + * Respond to adjustment event when horizontal or vertical scrollbar is + * changed * * @param evt - * DOCUMENT ME! + * adjustment event encoding whether hscroll or vscroll changed */ @Override public void adjustmentValueChanged(AdjustmentEvent evt) @@ -769,7 +774,16 @@ public class AlignmentPanel extends GAlignmentPanel implements @Override public void run() { - setScrollValues(vpRanges.getStartRes(), vpRanges.getStartSeq()); + // When updating scrolling to use ViewportChange events, this code + // could not be validated and it is not clear if it is now being + // called. Log warning here in case it is called and unforeseen + // problems occur + Cache.log + .warn("Unexpected path through code: Wrapped jar file opened with wrap alignment set in preferences"); + + // scroll to start of panel + vpRanges.setStartRes(0); + vpRanges.setStartSeq(0); } }); } @@ -872,7 +886,8 @@ public class AlignmentPanel extends GAlignmentPanel implements int maxwidth = av.getAlignment().getWidth(); if (av.hasHiddenColumns()) { - maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1; + maxwidth = av.getAlignment().getHiddenColumns() + .findColumnPosition(maxwidth) - 1; } // get the width of the canvas in residues @@ -1157,7 +1172,8 @@ public class AlignmentPanel extends GAlignmentPanel implements int maxwidth = av.getAlignment().getWidth(); if (av.hasHiddenColumns()) { - maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1; + maxwidth = av.getAlignment().getHiddenColumns() + .findColumnPosition(maxwidth) - 1; } int resWidth = getSeqPanel().seqCanvas.getWrappedCanvasWidth(pwidth @@ -1351,7 +1367,8 @@ public class AlignmentPanel extends GAlignmentPanel implements int maxwidth = av.getAlignment().getWidth(); if (av.hasHiddenColumns()) { - maxwidth = av.getColumnSelection().findColumnPosition(maxwidth); + maxwidth = av.getAlignment().getHiddenColumns() + .findColumnPosition(maxwidth); } int height = ((av.getAlignment().getHeight() + 1) * av.getCharHeight()) @@ -1581,7 +1598,8 @@ public class AlignmentPanel extends GAlignmentPanel implements int maxwidth = av.getAlignment().getWidth(); if (av.hasHiddenColumns()) { - maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1; + maxwidth = av.getAlignment().getHiddenColumns() + .findColumnPosition(maxwidth) - 1; } int height = ((maxwidth / chunkWidth) + 1) * cHeight; @@ -1599,6 +1617,8 @@ public class AlignmentPanel extends GAlignmentPanel implements PaintRefresher.RemoveComponent(getIdPanel().getIdCanvas()); PaintRefresher.RemoveComponent(this); + closeChildFrames(); + /* * try to ensure references are nulled */ @@ -1630,6 +1650,17 @@ public class AlignmentPanel extends GAlignmentPanel implements } /** + * Close any open dialogs that would be orphaned when this one is closed + */ + protected void closeChildFrames() + { + if (calculationDialog != null) + { + calculationDialog.closeFrame(); + } + } + + /** * hides or shows dynamic annotation rows based on groups and av state flags */ public void updateAnnotation() @@ -1827,14 +1858,19 @@ public class AlignmentPanel extends GAlignmentPanel implements * * @param b */ - protected void setDontScrollComplement(boolean b) + protected void setToScrollComplementPanel(boolean b) { - this.dontScrollComplement = b; + this.scrollComplementaryPanel = b; } - protected boolean isDontScrollComplement() + /** + * Get whether to scroll complement panel + * + * @return true if cDNA/protein complement panels should be scrolled + */ + protected boolean isSetToScrollComplementPanel() { - return this.dontScrollComplement; + return this.scrollComplementaryPanel; } /** @@ -1873,11 +1909,31 @@ public class AlignmentPanel extends GAlignmentPanel implements // now update any complementary alignment (its viewport ranges object // is different so does not get automatically updated) - if (!isDontScrollComplement()) + if (isSetToScrollComplementPanel()) { - setDontScrollComplement(true); + setToScrollComplementPanel(false); av.scrollComplementaryAlignment(); - setDontScrollComplement(false); + setToScrollComplementPanel(true); } } + + /** + * Set the reference to the PCA/Tree chooser dialog for this panel. This + * reference should be nulled when the dialog is closed. + * + * @param calculationChooser + */ + public void setCalculationDialog(CalculationChooser calculationChooser) + { + calculationDialog = calculationChooser; + } + + /** + * Returns the reference to the PCA/Tree chooser dialog for this panel (null + * if none is open) + */ + public CalculationChooser getCalculationDialog() + { + return calculationDialog; + } }