JAL-2388 Tidies

[jalview.git] / src / jalview / viewmodel / OverviewDimensions.java

diff --git a/src/jalview/viewmodel/OverviewDimensions.java b/src/jalview/viewmodel/OverviewDimensions.java
index 7c4ba9e..9a1e398 100644 (file)
--- a/src/jalview/viewmodel/OverviewDimensions.java
+++ b/src/jalview/viewmodel/OverviewDimensions.java
@@ -1,3 +1,23 @@
+/*
+ * 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;
@@ -10,12 +30,13 @@ 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,
@@ -148,16 +167,58 @@ 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
+   * @param ranges
+   *          the alignment's width and height ranges
+   */
   public abstract void updateViewportFromMouse(int mousex, int mousey,
           HiddenSequences hiddenSeqs, ColumnSelection hiddenCols,
           ViewportRanges ranges);
 
+  /**
+   * 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
+   * @param ranges
+   *          the alignment's width and height ranges
+   */
   public abstract void setBoxPosition(HiddenSequences hiddenSeqs,
           ColumnSelection hiddenCols, ViewportRanges ranges);
 
+  /**
+   * Get the collection of columns used by this overview dimensions object
+   * 
+   * @param ranges
+   *          the alignment's width and height ranges
+   * @param hiddenCols
+   *          the alignment's hidden columns
+   * @return a column collection
+   */
   public abstract AlignmentColsCollectionI getColumns(
           ViewportRanges ranges, ColumnSelection hiddenCols);
 
+  /**
+   * Get the collection of rows used by this overview dimensions object
+   * 
+   * @param ranges
+   *          the alignment's width and height ranges
+   * @param al
+   *          the alignment
+   * @return a row collection
+   */
   public abstract AlignmentRowsCollectionI getRows(
           ViewportRanges ranges, AlignmentI al);
 }
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