X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fviewmodel%2FOverviewDimensionsShowHidden.java;fp=src%2Fjalview%2Fviewmodel%2FOverviewDimensionsShowHidden.java;h=4f7d6c25bf70fff51eb6e1e9ff84930c4e5d491b;hb=c2e5d3d1ebe3b283bdde15637c590721cd6c5637;hp=0000000000000000000000000000000000000000;hpb=557859a3ea9a1e86899ef2033de90eadb6d87118;p=jalview.git

diff --git a/src/jalview/viewmodel/OverviewDimensionsShowHidden.java b/src/jalview/viewmodel/OverviewDimensionsShowHidden.java
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+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.viewmodel;
+
+import jalview.api.AlignmentColsCollectionI;
+import jalview.api.AlignmentRowsCollectionI;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.AllColsCollection;
+import jalview.datamodel.AllRowsCollection;
+import jalview.datamodel.HiddenColumns;
+import jalview.datamodel.HiddenSequences;
+
+public class OverviewDimensionsShowHidden extends OverviewDimensions
+{
+  private ViewportRanges ranges;
+
+  /**
+   * Create an OverviewDimensions object
+   * 
+   * @param ranges
+   *          positional properties of the viewport
+   * @param showAnnotationPanel
+   *          true if the annotation panel is to be shown, false otherwise
+   */
+  public OverviewDimensionsShowHidden(ViewportRanges vpranges,
+          boolean showAnnotationPanel)
+  {
+    super(vpranges, showAnnotationPanel);
+    ranges = vpranges;
+    resetAlignmentDims();
+  }
+
+  /**
+   * Check box dimensions and scroll positions and correct if necessary
+   * 
+   * @param mousex
+   *          x position in overview panel
+   * @param mousey
+   *          y position in overview panel
+   * @param hiddenSeqs
+   *          hidden sequences
+   * @param hiddenCols
+   *          hidden columns
+   * @param ranges
+   *          viewport position properties
+   */
+  @Override
+  public void updateViewportFromMouse(int mousex, int mousey,
+          HiddenSequences hiddenSeqs, HiddenColumns hiddenCols)
+  {
+    int x = mousex;
+    int y = mousey;
+
+    resetAlignmentDims();
+
+    if (x < 0)
+    {
+      x = 0;
+    }
+
+    if (y < 0)
+    {
+      y = 0;
+    }
+
+    //
+    // Convert x value to residue position
+    //
+
+    // need to determine where scrollCol should be, given x
+    // to do this also need to know width of viewport, and some hidden column
+    // correction
+
+    // convert x to residues - this is an absolute position
+    int xAsRes = Math.round((float) x * alwidth / width);
+
+    // get viewport width in residues
+    int vpwidth = ranges.getViewportWidth();
+
+    // get where x should be when accounting for hidden cols
+    // if x is in a hidden col region, shift to left - but we still need
+    // absolute position
+    // so convert back after getting visible region position
+    int visXAsRes = hiddenCols.findColumnPosition(xAsRes);
+
+    // check in case we went off the edge of the alignment
+    int visAlignWidth = hiddenCols.findColumnPosition(alwidth - 1);
+    if (visXAsRes + vpwidth - 1 > visAlignWidth)
+    {
+      // went past the end of the alignment, adjust backwards
+
+      // if last position was before the end of the alignment, need to update
+      if ((ranges.getEndRes() + vpwidth - 1) < visAlignWidth)
+      {
+        visXAsRes = hiddenCols.findColumnPosition(hiddenCols
+                .subtractVisibleColumns(vpwidth - 1, alwidth - 1));
+      }
+      else
+      {
+        visXAsRes = ranges.getEndRes();
+      }
+    }
+
+    //
+    // Convert y value to sequence position
+    //
+
+    // convert y to residues
+    int yAsSeq = Math.round((float) y * alheight / sequencesHeight);
+
+    // get viewport height in sequences
+    int vpheight = ranges.getViewportHeight();
+
+    // get where y should be when accounting for hidden rows
+    // if y is in a hidden row region, shift up - but we still need absolute
+    // position,
+    // so convert back after getting visible region position
+    yAsSeq = hiddenSeqs.adjustForHiddenSeqs(hiddenSeqs
+            .findIndexWithoutHiddenSeqs(yAsSeq));
+
+    // check in case we went off the edge of the alignment
+    int visAlignHeight = hiddenSeqs.findIndexWithoutHiddenSeqs(alheight);
+    int visYAsSeq = hiddenSeqs.findIndexWithoutHiddenSeqs(yAsSeq);
+    if (visYAsSeq + vpheight - 1 > visAlignHeight)
+    {
+      // went past the end of the alignment, adjust backwards
+      if ((ranges.getEndSeq() + vpheight - 1) < visAlignHeight)
+      {
+        visYAsSeq = hiddenSeqs.findIndexWithoutHiddenSeqs(hiddenSeqs
+                .subtractVisibleRows(vpheight - 1, alheight - 1));
+      }
+      else
+      {
+        visYAsSeq = ranges.getEndSeq();
+      }
+    }
+
+    // update viewport
+    ranges.setStartRes(xAsRes);
+    ranges.setStartSeq(yAsSeq);
+
+  }
+
+  /**
+   * Update the overview panel box when the associated alignment panel is
+   * changed
+   * 
+   * @param hiddenSeqs
+   *          hidden sequences
+   * @param hiddenCols
+   *          hidden columns
+   * @param ranges
+   *          viewport position properties
+   */
+  @Override
+  public void setBoxPosition(HiddenSequences hiddenSeqs,
+          HiddenColumns hiddenCols)
+  {
+    // work with absolute values of startRes and endRes
+    int startRes = hiddenCols
+            .adjustForHiddenColumns(ranges.getStartRes());
+    int endRes = hiddenCols.adjustForHiddenColumns(ranges.getEndRes());
+
+    // work with absolute values of startSeq and endSeq
+    int startSeq = hiddenSeqs.adjustForHiddenSeqs(ranges.getStartSeq());
+    int endSeq = hiddenSeqs.adjustForHiddenSeqs(ranges.getEndSeq());
+
+    setBoxPosition(startRes, endRes, startSeq, endSeq);
+  }
+
+  @Override
+  public AlignmentColsCollectionI getColumns(AlignmentI al)
+  {
+    return new AllColsCollection(0,
+            ranges.getAbsoluteAlignmentWidth() - 1, al);
+  }
+
+  @Override
+  public AlignmentRowsCollectionI getRows(AlignmentI al)
+  {
+    return new AllRowsCollection(0,
+            ranges.getAbsoluteAlignmentHeight() - 1,
+            al);
+  }
+
+  @Override
+  protected void resetAlignmentDims()
+  {
+    alwidth = ranges.getAbsoluteAlignmentWidth();
+    alheight = ranges.getAbsoluteAlignmentHeight();
+  }
+}