X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fviewmodel%2FOverviewDimensions.java;h=a837d53b83d6d435b9d4218ea160c5505acc09c2;hb=968c3bcde941e502fcf7d497343600f4f58f6c9a;hp=7c4ba9ee80ccad8501cbbd3382d39316cdc45a3e;hpb=cdd071033b669ae1489f3bba67c4a0a041776b31;p=jalview.git

diff --git a/src/jalview/viewmodel/OverviewDimensions.java b/src/jalview/viewmodel/OverviewDimensions.java
index 7c4ba9e..a837d53 100644
--- a/src/jalview/viewmodel/OverviewDimensions.java
+++ b/src/jalview/viewmodel/OverviewDimensions.java
@@ -1,21 +1,42 @@
+/*
+ * 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.ColumnSelection;
+import jalview.datamodel.HiddenColumns;
 import jalview.datamodel.HiddenSequences;
 
 import java.awt.Graphics;
 
 public abstract class OverviewDimensions
 {
-
-  private static final int DEFAULT_GRAPH_HEIGHT = 20;
   protected static final int MAX_WIDTH = 400;
   protected static final int MIN_WIDTH = 120;
   protected static final int MIN_SEQ_HEIGHT = 40;
   protected static final int MAX_SEQ_HEIGHT = 300;
+
+  private static final int DEFAULT_GRAPH_HEIGHT = 20;
+
   protected int width;
   protected int sequencesHeight;
   protected int graphHeight = DEFAULT_GRAPH_HEIGHT;
@@ -25,9 +46,7 @@ public abstract class OverviewDimensions
   protected int boxHeight = -1;
   protected int scrollCol = -1;
   protected int scrollRow = -1;
-
   protected int alwidth;
-
   protected int alheight;
 
   public OverviewDimensions(ViewportRanges ranges,
@@ -130,11 +149,13 @@ public abstract class OverviewDimensions
 
   public float getPixelsPerCol()
   {
+    resetAlignmentDims();
     return (float) width / alwidth;
   }
 
   public float getPixelsPerSeq()
   {
+    resetAlignmentDims();
     return (float) sequencesHeight / alheight;
   }
 
@@ -148,16 +169,71 @@ public abstract class OverviewDimensions
     sequencesHeight = h - graphHeight;
   }
 
+  /**
+   * Update the viewport location from a mouse click in the overview panel
+   * 
+   * @param mousex
+   *          x location of mouse
+   * @param mousey
+   *          y location of mouse
+   * @param hiddenSeqs
+   *          the alignment's hidden sequences
+   * @param hiddenCols
+   *          the alignment's hidden columns
+   */
   public abstract void updateViewportFromMouse(int mousex, int mousey,
-          HiddenSequences hiddenSeqs, ColumnSelection hiddenCols,
-          ViewportRanges ranges);
+          HiddenSequences hiddenSeqs, HiddenColumns hiddenCols);
 
+  /**
+   * Set the overview panel's box position to match the viewport
+   * 
+   * @param hiddenSeqs
+   *          the alignment's hidden sequences
+   * @param hiddenCols
+   *          the alignment's hidden columns
+   */
   public abstract void setBoxPosition(HiddenSequences hiddenSeqs,
-          ColumnSelection hiddenCols, ViewportRanges ranges);
+          HiddenColumns hiddenCols);
 
-  public abstract AlignmentColsCollectionI getColumns(
-          ViewportRanges ranges, ColumnSelection hiddenCols);
+  /**
+   * Get the collection of columns used by this overview dimensions object
+   * 
+   * @param hiddenCols
+   *          the alignment's hidden columns
+   * @return a column collection
+   */
+  public abstract AlignmentColsCollectionI getColumns(AlignmentI al);
 
-  public abstract AlignmentRowsCollectionI getRows(
-          ViewportRanges ranges, AlignmentI al);
+  /**
+   * Get the collection of rows used by this overview dimensions object
+   * 
+   * @param al
+   *          the alignment
+   * @return a row collection
+   */
+  public abstract AlignmentRowsCollectionI getRows(AlignmentI al);
+
+  /**
+   * Updates overview dimensions to account for current alignment dimensions
+   */
+  protected abstract void resetAlignmentDims();
+
+  protected void setBoxPosition(int startRes, int endRes, int startSeq,
+          int endSeq)
+  {
+    resetAlignmentDims();
+
+    // boxX, boxY is the x,y location equivalent to startRes, startSeq
+    boxX = Math.round((float) startRes * width / alwidth);
+    boxY = Math.round((float) startSeq * sequencesHeight / alheight);
+
+    // boxWidth is the width in residues translated to pixels
+    // since the box includes both the start and end residues, add 1 to the
+    // difference
+    boxWidth = Math
+            .round((float) (endRes - startRes + 1) * width / alwidth);
+    // boxHeight is the height in sequences translated to pixels
+    boxHeight = Math.round((float) (endSeq - startSeq + 1)
+            * sequencesHeight / alheight);
+  }
 }
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