X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignmentPanel.java;fp=src%2Fjalview%2Fgui%2FAlignmentPanel.java;h=ac137b9ab455a23b493a166b94ce308385141ac5;hb=d5bcc3830eab04e6db816e1c2ad8fce1dc189612;hp=e61b042728f4735e45ab91592db20f2ae4817703;hpb=3ebdd4e28382e38a181aae1eed71549f603f9025;p=jalview.git diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java index e61b042..ac137b9 100644 --- a/src/jalview/gui/AlignmentPanel.java +++ b/src/jalview/gui/AlignmentPanel.java @@ -35,6 +35,7 @@ import jalview.schemes.ResidueProperties; import jalview.structure.StructureSelectionManager; import jalview.util.MessageManager; import jalview.util.Platform; +import jalview.viewmodel.ViewportRanges; import java.awt.BorderLayout; import java.awt.Color; @@ -69,6 +70,8 @@ public class AlignmentPanel extends GAlignmentPanel implements { public AlignViewport av; + ViewportRanges vpRanges; + OverviewPanel overviewPanel; private SeqPanel seqPanel; @@ -91,9 +94,9 @@ public class AlignmentPanel extends GAlignmentPanel implements // this value is set false when selection area being dragged boolean fastPaint = true; - int hextent = 0; + private int hextent = 0; - int vextent = 0; + private int vextent = 0; /* * Flag set while scrolling to follow complementary cDNA/protein scroll. When @@ -113,6 +116,7 @@ public class AlignmentPanel extends GAlignmentPanel implements { alignFrame = af; this.av = av; + vpRanges = av.getRanges(); setSeqPanel(new SeqPanel(av, this)); setIdPanel(new IdPanel(av, this)); @@ -377,7 +381,7 @@ public class AlignmentPanel extends GAlignmentPanel implements */ if (centre) { - int offset = (av.getEndRes() - av.getStartRes() + 1) / 2 - 1; + int offset = (vpRanges.getEndRes() - vpRanges.getStartRes() + 1) / 2 - 1; start = Math.max(start - offset, 0); end = end + offset - 1; } @@ -413,7 +417,7 @@ public class AlignmentPanel extends GAlignmentPanel implements // + av.getStartSeq() + ", ends=" + av.getEndSeq()); if (!av.getWrapAlignment()) { - if ((startv = av.getStartRes()) >= start) + if ((startv = vpRanges.getStartRes()) >= start) { /* * Scroll left to make start of search results visible @@ -421,7 +425,7 @@ public class AlignmentPanel extends GAlignmentPanel implements // setScrollValues(start - 1, seqIndex); // plus one residue setScrollValues(start, seqIndex); } - else if ((endv = av.getEndRes()) <= end) + else if ((endv = vpRanges.getEndRes()) <= end) { /* * Scroll right to make end of search results visible @@ -429,19 +433,20 @@ public class AlignmentPanel extends GAlignmentPanel implements // setScrollValues(startv + 1 + end - endv, seqIndex); // plus one setScrollValues(startv + end - endv, seqIndex); } - else if ((starts = av.getStartSeq()) > seqIndex) + else if ((starts = vpRanges.getStartSeq()) > seqIndex) { /* * Scroll up to make start of search results visible */ - setScrollValues(av.getStartRes(), seqIndex); + setScrollValues(vpRanges.getStartRes(), seqIndex); } - else if ((ends = av.getEndSeq()) <= seqIndex) + else if ((ends = vpRanges.getEndSeq()) <= seqIndex) { /* * Scroll down to make end of search results visible */ - setScrollValues(av.getStartRes(), starts + seqIndex - ends + 1); + setScrollValues(vpRanges.getStartRes(), starts + seqIndex - ends + + 1); } /* * Else results are already visible - no need to scroll @@ -464,10 +469,11 @@ public class AlignmentPanel extends GAlignmentPanel implements { int cwidth = getSeqPanel().seqCanvas .getWrappedCanvasWidth(getSeqPanel().seqCanvas.getWidth()); - if (res < av.getStartRes() || res >= (av.getStartRes() + cwidth)) + if (res < vpRanges.getStartRes() + || res >= (vpRanges.getStartRes() + cwidth)) { vscroll.setValue((res / cwidth)); - av.startRes = vscroll.getValue() * cwidth; + vpRanges.setStartRes(vscroll.getValue() * cwidth); } } @@ -591,7 +597,7 @@ public class AlignmentPanel extends GAlignmentPanel implements fontChanged(); setAnnotationVisible(av.isShowAnnotation()); boolean wrap = av.getWrapAlignment(); - av.startSeq = 0; + vpRanges.setStartSeq(0); scalePanelHolder.setVisible(!wrap); hscroll.setVisible(!wrap); idwidthAdjuster.setVisible(!wrap); @@ -688,7 +694,6 @@ public class AlignmentPanel extends GAlignmentPanel implements */ public void setScrollValues(int x, int y) { - // System.err.println("Scroll " + this.av.viewName + " to " + x + "," + y); if (av == null || av.getAlignment() == null) { return; @@ -698,12 +703,10 @@ public class AlignmentPanel extends GAlignmentPanel implements if (av.hasHiddenColumns()) { + // reset the width to exclude hidden columns width = av.getColumnSelection().findColumnPosition(width); } - av.setEndRes((x + (getSeqPanel().seqCanvas.getWidth() / av - .getCharWidth())) - 1); - hextent = getSeqPanel().seqCanvas.getWidth() / av.getCharWidth(); vextent = getSeqPanel().seqCanvas.getHeight() / av.getCharHeight(); @@ -737,6 +740,10 @@ public class AlignmentPanel extends GAlignmentPanel implements x = 0; } + // update endRes after x has (possibly) been adjusted + vpRanges.setEndRes((x + (getSeqPanel().seqCanvas.getWidth() / av + .getCharWidth())) - 1); + /* * each scroll adjustment triggers adjustmentValueChanged, which resets the * 'do not scroll complement' flag; ensure it is the same for both @@ -757,14 +764,14 @@ public class AlignmentPanel extends GAlignmentPanel implements @Override public void adjustmentValueChanged(AdjustmentEvent evt) { - int oldX = av.getStartRes(); - int oldY = av.getStartSeq(); + int oldX = vpRanges.getStartRes(); + int oldY = vpRanges.getStartSeq(); if (evt.getSource() == hscroll) { int x = hscroll.getValue(); - av.setStartRes(x); - av.setEndRes((x + (getSeqPanel().seqCanvas.getWidth() / av + vpRanges.setStartRes(x); + vpRanges.setEndRes((x + (getSeqPanel().seqCanvas.getWidth() / av .getCharWidth())) - 1); } @@ -778,8 +785,8 @@ public class AlignmentPanel extends GAlignmentPanel implements { int rowSize = getSeqPanel().seqCanvas .getWrappedCanvasWidth(getSeqPanel().seqCanvas.getWidth()); - av.setStartRes(offy * rowSize); - av.setEndRes((offy + 1) * rowSize); + vpRanges.setStartRes(offy * rowSize); + vpRanges.setEndRes((offy + 1) * rowSize); } else { @@ -791,16 +798,18 @@ public class AlignmentPanel extends GAlignmentPanel implements @Override public void run() { - setScrollValues(av.getStartRes(), av.getStartSeq()); + setScrollValues(vpRanges.getStartRes(), + vpRanges.getStartSeq()); } }); } } else { - av.setStartSeq(offy); - av.setEndSeq(offy - + (getSeqPanel().seqCanvas.getHeight() / av.getCharHeight())); + vpRanges.setStartSeq(offy); + vpRanges.setEndSeq(offy + + (getSeqPanel().seqCanvas.getHeight() / av.getCharHeight()) + - 1); } } @@ -809,8 +818,8 @@ public class AlignmentPanel extends GAlignmentPanel implements overviewPanel.setBoxPosition(); } - int scrollX = av.startRes - oldX; - int scrollY = av.startSeq - oldY; + int scrollX = vpRanges.getStartRes() - oldX; + int scrollY = vpRanges.getStartSeq() - oldY; if (av.getWrapAlignment() || !fastPaint) { @@ -820,13 +829,13 @@ public class AlignmentPanel extends GAlignmentPanel implements { // Make sure we're not trying to draw a panel // larger than the visible window - if (scrollX > av.endRes - av.startRes) + if (scrollX > vpRanges.getEndRes() - vpRanges.getStartRes()) { - scrollX = av.endRes - av.startRes; + scrollX = vpRanges.getEndRes() - vpRanges.getStartRes(); } - else if (scrollX < av.startRes - av.endRes) + else if (scrollX < vpRanges.getStartRes() - vpRanges.getEndRes()) { - scrollX = av.startRes - av.endRes; + scrollX = vpRanges.getStartRes() - vpRanges.getEndRes(); } if (scrollX != 0 || scrollY != 0) @@ -926,7 +935,7 @@ public class AlignmentPanel extends GAlignmentPanel implements } else { - setScrollValues(av.getStartRes(), av.getStartSeq()); + setScrollValues(vpRanges.getStartRes(), vpRanges.getStartSeq()); } }