X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignmentPanel.java;h=395f6b3a253eed1b6524f2e381799abd1a8cf657;hb=d8ca2529b8e334195e29723211fb05e84bac6e03;hp=795146d8f41b5432b727e9e4d44946369b6583d2;hpb=cf6307d618f73e86688f091f213a07f0b8820917;p=jalview.git diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java index 795146d..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. * @@ -152,16 +155,22 @@ public class AlignmentPanel extends GAlignmentPanel implements // reset the viewport ranges when the alignment panel is resized // in particular, this initialises the end residue value when Jalview // is initialised - int widthInRes = (getSeqPanel().seqCanvas.getWidth() / av - .getCharWidth()) - 1; - int currentStartRes = vpRanges.getStartRes(); if (av.getWrapAlignment()) { - widthInRes = getSeqPanel().seqCanvas + int widthInRes = getSeqPanel().seqCanvas .getWrappedCanvasWidth(getSeqPanel().seqCanvas.getWidth()); + vpRanges.setViewportWidth(widthInRes); + } + else + { + int widthInRes = getSeqPanel().seqCanvas.getWidth() + / av.getCharWidth(); + int heightInSeq = getSeqPanel().seqCanvas.getHeight() + / av.getCharHeight(); + + vpRanges.setViewportWidth(widthInRes); + vpRanges.setViewportHeight(heightInSeq); } - - vpRanges.setStartEndRes(currentStartRes, widthInRes); } }); @@ -197,6 +206,11 @@ public class AlignmentPanel extends GAlignmentPanel implements { av.alignmentChanged(this); + if (getCalculationDialog() != null) + { + getCalculationDialog().validateCalcTypes(); + } + alignFrame.updateEditMenuBar(); paintAlignment(true); @@ -227,10 +241,6 @@ public class AlignmentPanel extends GAlignmentPanel implements getIdPanel().getIdCanvas().setPreferredSize(d); hscrollFillerPanel.setPreferredSize(d); - if (overviewPanel != null) - { - overviewPanel.setBoxPosition(); - } if (this.alignFrame.getSplitViewContainer() != null) { ((SplitFrame) this.alignFrame.getSplitViewContainer()).adjustLayout(); @@ -399,9 +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 @@ -409,7 +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; } @@ -423,11 +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; @@ -440,9 +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) @@ -450,7 +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) @@ -458,7 +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) @@ -482,29 +486,14 @@ public class AlignmentPanel extends GAlignmentPanel implements } else { - scrollToWrappedVisible(start); + vpRanges.scrollToWrappedVisible(start); } } - if (redrawOverview && overviewPanel != null) - { - overviewPanel.setBoxPosition(); - } + paintAlignment(redrawOverview); return true; } - void scrollToWrappedVisible(int res) - { - int cwidth = getSeqPanel().seqCanvas - .getWrappedCanvasWidth(getSeqPanel().seqCanvas.getWidth()); - if (res < vpRanges.getStartRes() - || res >= (vpRanges.getStartRes() + cwidth)) - { - vscroll.setValue((res / cwidth)); - } - - } - /** * DOCUMENT ME! * @@ -640,75 +629,28 @@ public class AlignmentPanel extends GAlignmentPanel implements annotationSpaceFillerHolder.setVisible(true); } - idSpaceFillerPanel1.setVisible(!wrap); - - repaint(); - } - - // return value is true if the scroll is valid - public boolean scrollUp(boolean up) - { - if (up) + if (wrap) { - if (vscroll.getValue() < 1) - { - return false; - } - - fastPaint = false; - vscroll.setValue(vscroll.getValue() - 1); + int widthInRes = getSeqPanel().seqCanvas + .getWrappedCanvasWidth(getSeqPanel().seqCanvas.getWidth()); + vpRanges.setViewportWidth(widthInRes); } else { - if ((vextent + vscroll.getValue()) >= av.getAlignment().getHeight()) - { - return false; - } + int widthInRes = (getSeqPanel().seqCanvas.getWidth() / av + .getCharWidth()) - 1; + int heightInSeq = (getSeqPanel().seqCanvas.getHeight() / av + .getCharHeight()) - 1; - fastPaint = false; - vscroll.setValue(vscroll.getValue() + 1); + vpRanges.setViewportWidth(widthInRes); + vpRanges.setViewportHeight(heightInSeq); } - fastPaint = true; + idSpaceFillerPanel1.setVisible(!wrap); - return true; + repaint(); } - /** - * DOCUMENT ME! - * - * @param right - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public boolean scrollRight(boolean right) - { - if (!right) - { - if (hscroll.getValue() < 1) - { - return false; - } - - fastPaint = false; - hscroll.setValue(hscroll.getValue() - 1); - } - else - { - if ((hextent + hscroll.getValue()) >= av.getAlignment().getWidth()) - { - return false; - } - - fastPaint = false; - hscroll.setValue(hscroll.getValue() + 1); - } - - fastPaint = true; - - return true; - } /** * Adjust row/column scrollers to show a visible position in the alignment. @@ -719,8 +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; @@ -732,14 +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(); @@ -782,16 +726,19 @@ 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) { int oldX = vpRanges.getStartRes(); + int oldwidth = vpRanges.getViewportWidth(); int oldY = vpRanges.getStartSeq(); + int oldheight = vpRanges.getViewportHeight(); if (av.getWrapAlignment()) { @@ -808,29 +755,37 @@ public class AlignmentPanel extends GAlignmentPanel implements // if we're scrolling to the position we're already at, stop // this prevents infinite recursion of events when the scroll/viewport // ranges values are the same - if (offy * rowSize == oldX) + if ((offy * rowSize == oldX) && (oldwidth == rowSize)) { return; } else if (offy > -1) { - vpRanges.setStartEndRes(offy * rowSize, (offy + 1) * rowSize); + vpRanges.setViewportStartAndWidth(offy * rowSize, rowSize); } - else + } + else + { + // This is only called if file loaded is a jar file that + // was wrapped when saved and user has wrap alignment true + // as preference setting + SwingUtilities.invokeLater(new Runnable() { - // This is only called if file loaded is a jar file that - // was wrapped when saved and user has wrap alignment true - // as preference setting - SwingUtilities.invokeLater(new Runnable() - { - @Override - public void run() - { - setScrollValues(vpRanges.getStartRes(), - vpRanges.getStartSeq()); - } - }); - } + @Override + public void run() + { + // 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); + } + }); } repaint(); } @@ -840,34 +795,31 @@ public class AlignmentPanel extends GAlignmentPanel implements if (evt.getSource() == hscroll) { int x = hscroll.getValue(); + int width = getSeqPanel().seqCanvas.getWidth() / av.getCharWidth(); // if we're scrolling to the position we're already at, stop // this prevents infinite recursion of events when the scroll/viewport // ranges values are the same - if (x == oldX) + if ((x == oldX) && (width == oldwidth)) { return; } - vpRanges.setStartEndRes(x, - (x + (getSeqPanel().seqCanvas.getWidth() / av - .getCharWidth())) - 1); + vpRanges.setViewportStartAndWidth(x, width); } else if (evt.getSource() == vscroll) { - int offy = vscroll.getValue(); + int y = vscroll.getValue(); + int height = getSeqPanel().seqCanvas.getHeight() + / av.getCharHeight(); // if we're scrolling to the position we're already at, stop // this prevents infinite recursion of events when the scroll/viewport // ranges values are the same - if (offy == oldY) + if ((y == oldY) && (height == oldheight)) { return; } - vpRanges.setStartEndSeq( - offy, - offy - + (getSeqPanel().seqCanvas.getHeight() / av - .getCharHeight()) - 1); + vpRanges.setViewportStartAndHeight(y, height); } if (!fastPaint) { @@ -934,7 +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 @@ -1219,7 +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 @@ -1413,7 +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()) @@ -1643,7 +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; @@ -1661,6 +1617,8 @@ public class AlignmentPanel extends GAlignmentPanel implements PaintRefresher.RemoveComponent(getIdPanel().getIdCanvas()); PaintRefresher.RemoveComponent(this); + closeChildFrames(); + /* * try to ensure references are nulled */ @@ -1692,6 +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() @@ -1889,14 +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; } /** @@ -1935,11 +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; + } }