X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FAnnotationColourGradient.java;h=1422ce54380c2723148ec20efa98a5643057e115;hb=ab43013b7e357b84b4abade0dba949668dfb2a0e;hp=d91ced5ba9debf97f9804a7a140a52703b027790;hpb=afe9d37d27d5621b0b2a60516646a353e45525b6;p=jalview.git

diff --git a/src/jalview/schemes/AnnotationColourGradient.java b/src/jalview/schemes/AnnotationColourGradient.java
index d91ced5..1422ce5 100755
--- a/src/jalview/schemes/AnnotationColourGradient.java
+++ b/src/jalview/schemes/AnnotationColourGradient.java
@@ -1,123 +1,410 @@
-/*
-* Jalview - A Sequence Alignment Editor and Viewer
-* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
-*
-* This program 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 2
-* of the License, or (at your option) any later version.
-*
-* This program 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 this program; if not, write to the Free Software
-* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
-*/
-package jalview.schemes;
-
-import java.awt.*;
-
-import jalview.datamodel.*;
-
-public class AnnotationColourGradient extends ResidueColourScheme
-{
-    AlignmentAnnotation annotation;
-    boolean aboveAnnotationThreshold = false;
-
-    float r1, g1, b1, rr, gg, bb, dr, dg, db;
-    float range;
-
-    /**
-     * Creates a new AnnotationColourGradient object.
-     */
-    public AnnotationColourGradient(AlignmentAnnotation annotation,
-        Color minColour, Color maxColour, boolean aboveThreshold)
-    {
-      this.annotation = annotation;
-
-      aboveAnnotationThreshold = aboveThreshold;
-
-      r1 = minColour.getRed();
-      g1 = minColour.getGreen();
-      b1 = minColour.getBlue();
-
-      rr = maxColour.getRed() - r1;
-      gg = maxColour.getGreen() - g1;
-      bb = maxColour.getBlue() - b1;
-
-      range = annotation.graphMax - annotation.graphMin;
-
-    }
-
-    public Color getMinColour()
-    {
-      return new Color( (int) r1, (int) g1, (int) b1);
-    }
-
-    public Color getMaxColour()
-    {
-      return new Color( (int) (r1 + rr), (int) (g1 + gg), (int) (b1 + bb));
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param n DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public Color findColour(String n)
-    {
-      System.out.println("AnnotationColourGradient findColour(string)");
-        return Color.RED;
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param n DOCUMENT ME!
-     * @param j DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public Color findColour(String n, int j)
-    {
-        if ((threshold == 0) || aboveThreshold(n, j))
-        {
-          if(annotation.annotations[j]==null)
-            currentColour = Color.white;
-          else
-          {
-            if(!aboveAnnotationThreshold || (annotation.graphLines!=null
-               && annotation.annotations[j].value>=annotation.getGraphLine(0).value))
-            {
-                dr = rr *
-                     ((annotation.annotations[j].value-annotation.graphMin) / range )
-                     +r1;
-                dg = gg *
-                     ((annotation.annotations[j].value-annotation.graphMin)  / range )
-                     +g1;
-                db = bb *
-                     ((annotation.annotations[j].value-annotation.graphMin) / range )
-                     +b1;
-
-                 currentColour = new Color( (int) dr, (int) dg, (int) db);
-            }
-            else
-              currentColour = Color.white;
-          }
-        }
-        else
-        {
-            return Color.white;
-        }
-
-        if(conservationColouring)
-         applyConservation(j);
-
-       return currentColour;
-    }
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
+ * Copyright (C) 2014 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.schemes;
+
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.AnnotatedCollectionI;
+import jalview.datamodel.Annotation;
+import jalview.datamodel.GraphLine;
+import jalview.datamodel.SequenceCollectionI;
+import jalview.datamodel.SequenceI;
+
+import java.awt.Color;
+import java.util.IdentityHashMap;
+import java.util.Map;
+
+public class AnnotationColourGradient extends FollowerColourScheme
+{
+  public static final int NO_THRESHOLD = -1;
+
+  public static final int BELOW_THRESHOLD = 0;
+
+  public static final int ABOVE_THRESHOLD = 1;
+
+  public AlignmentAnnotation annotation;
+
+  int aboveAnnotationThreshold = -1;
+
+  public boolean thresholdIsMinMax = false;
+
+  GraphLine annotationThreshold;
+
+  float r1, g1, b1, rr, gg, bb;
+
+  private boolean predefinedColours = false;
+
+  private boolean seqAssociated = false;
+  /**
+   * false if the scheme was constructed without a minColour and maxColour used
+   * to decide if existing colours should be taken from annotation elements when
+   * they exist
+   */
+  private boolean noGradient = false;
+  IdentityHashMap<SequenceI, AlignmentAnnotation> seqannot = null;
+
+  @Override
+  public ColourSchemeI applyTo(AnnotatedCollectionI sg,
+          Map<SequenceI, SequenceCollectionI> hiddenRepSequences)
+  {
+    AnnotationColourGradient acg = new AnnotationColourGradient(annotation,
+            colourScheme, aboveAnnotationThreshold);
+    acg.thresholdIsMinMax = thresholdIsMinMax;
+    acg.annotationThreshold = (annotationThreshold == null) ? null
+            : new GraphLine(annotationThreshold);
+    acg.r1 = r1;
+    acg.g1 = g1;
+    acg.b1 = b1;
+    acg.rr = rr;
+    acg.gg = gg;
+    acg.bb = bb;
+    acg.predefinedColours = predefinedColours;
+    acg.seqAssociated = seqAssociated;
+    acg.noGradient = noGradient;
+    return acg;
+  }
+
+  /**
+   * Creates a new AnnotationColourGradient object.
+   */
+  public AnnotationColourGradient(AlignmentAnnotation annotation,
+          ColourSchemeI originalColour, int aboveThreshold)
+  {
+    if (originalColour instanceof AnnotationColourGradient)
+    {
+      colourScheme = ((AnnotationColourGradient) originalColour).colourScheme;
+    }
+    else
+    {
+      colourScheme = originalColour;
+    }
+
+    this.annotation = annotation;
+
+    aboveAnnotationThreshold = aboveThreshold;
+
+    if (aboveThreshold != NO_THRESHOLD && annotation.threshold != null)
+    {
+      annotationThreshold = annotation.threshold;
+    }
+    // clear values so we don't get weird black bands...
+    r1 = 254;
+    g1 = 254;
+    b1 = 254;
+    rr = 0;
+    gg = 0;
+    bb = 0;
+
+    noGradient = true;
+  }
+
+  /**
+   * Creates a new AnnotationColourGradient object.
+   */
+  public AnnotationColourGradient(AlignmentAnnotation annotation,
+          Color minColour, Color maxColour, int aboveThreshold)
+  {
+    this.annotation = annotation;
+
+    aboveAnnotationThreshold = aboveThreshold;
+
+    if (aboveThreshold != NO_THRESHOLD && annotation.threshold != null)
+    {
+      annotationThreshold = annotation.threshold;
+    }
+
+    r1 = minColour.getRed();
+    g1 = minColour.getGreen();
+    b1 = minColour.getBlue();
+
+    rr = maxColour.getRed() - r1;
+    gg = maxColour.getGreen() - g1;
+    bb = maxColour.getBlue() - b1;
+
+    noGradient = false;
+    aamax = annotation.graphMax;
+    aamin = annotation.graphMin;
+    if (annotation.isRNA())
+    {
+      ColourSchemeProperty.initRnaHelicesShading(1 + (int) aamax);
+    }
+  }
+
+  @Override
+  public void alignmentChanged(AnnotatedCollectionI alignment,
+          Map<SequenceI, SequenceCollectionI> hiddenReps)
+  {
+    super.alignmentChanged(alignment, hiddenReps);
+
+    if (seqAssociated && annotation.getCalcId() != null)
+    {
+      if (seqannot != null)
+      {
+        seqannot.clear();
+      }
+      else
+      {
+        seqannot = new IdentityHashMap<SequenceI, AlignmentAnnotation>();
+      }
+      // resolve the context containing all the annotation for the sequence
+      AnnotatedCollectionI alcontext = alignment instanceof AlignmentI ? alignment
+              : alignment.getContext();
+      boolean f = true,rna=false;
+      for (AlignmentAnnotation alan : alcontext.findAnnotation(annotation
+              .getCalcId()))
+      {
+        if (alan.sequenceRef != null
+                && (alan.label != null && annotation != null && alan.label
+                        .equals(annotation.label)))
+        {
+          if (!rna && alan.isRNA())
+          {
+            rna = true;
+          }
+          seqannot.put(alan.sequenceRef, alan);
+          if (f || alan.graphMax > aamax)
+          {
+            aamax = alan.graphMax;
+          }
+          if (f || alan.graphMin < aamin)
+          {
+            aamin = alan.graphMin;
+          }
+          f = false;
+        }
+      }
+      if (rna)
+      {
+        ColourSchemeProperty.initRnaHelicesShading(1 + (int) aamax);
+      }
+    }
+  }
+
+  float aamin = 0f, aamax = 0f;
+  public String getAnnotation()
+  {
+    return annotation.label;
+  }
+
+  public int getAboveThreshold()
+  {
+    return aboveAnnotationThreshold;
+  }
+
+  public float getAnnotationThreshold()
+  {
+    if (annotationThreshold == null)
+    {
+      return 0;
+    }
+    else
+    {
+      return annotationThreshold.value;
+    }
+  }
+
+  public Color getMinColour()
+  {
+    return new Color((int) r1, (int) g1, (int) b1);
+  }
+
+  public Color getMaxColour()
+  {
+    return new Color((int) (r1 + rr), (int) (g1 + gg), (int) (b1 + bb));
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param n
+   *          DOCUMENT ME!
+   * 
+   * @return DOCUMENT ME!
+   */
+  public Color findColour(char c)
+  {
+    return Color.red;
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param n
+   *          DOCUMENT ME!
+   * @param j
+   *          DOCUMENT ME!
+   * 
+   * @return DOCUMENT ME!
+   */
+  @Override
+  public Color findColour(char c, int j, SequenceI seq)
+  {
+    Color currentColour = Color.white;
+    AlignmentAnnotation annotation = (seqAssociated ? seqannot.get(seq)
+            : this.annotation);
+    if (annotation == null)
+    {
+      return currentColour;
+    }
+    if ((threshold == 0) || aboveThreshold(c, j))
+    {
+      if (annotation.annotations != null
+              && j < annotation.annotations.length
+              && annotation.annotations[j] != null
+              && !jalview.util.Comparison.isGap(c))
+      {
+        Annotation aj = annotation.annotations[j];
+        // 'use original colours' => colourScheme != null
+        // -> look up colour to be used
+        // predefined colours => preconfigured shading
+        // -> only use original colours reference if thresholding enabled &
+        // minmax exists
+        // annotation.hasIcons => null or black colours replaced with glyph
+        // colours
+        // -> reuse original colours if present
+        // -> if thresholding enabled then return colour on non-whitespace glyph
+
+        if (aboveAnnotationThreshold == NO_THRESHOLD
+                || (annotationThreshold != null && (aboveAnnotationThreshold == ABOVE_THRESHOLD ? aj.value >= annotationThreshold.value
+                        : aj.value <= annotationThreshold.value)))
+        {
+          if (predefinedColours && aj.colour != null
+                  && !aj.colour.equals(Color.black))
+          {
+            currentColour = aj.colour;
+          }
+          else if (annotation.hasIcons
+                  && annotation.graph == AlignmentAnnotation.NO_GRAPH)
+          {
+            if (aj.secondaryStructure > ' ' && aj.secondaryStructure != '.'
+                    && aj.secondaryStructure != '-')
+            {
+              if (colourScheme != null)
+              {
+                currentColour = colourScheme.findColour(c, j, seq);
+              }
+              else
+              {
+                if (annotation.isRNA())
+                {
+                  currentColour = ColourSchemeProperty.rnaHelices[(int) aj.value];
+                }
+                else
+                {
+                  currentColour = annotation.annotations[j].secondaryStructure == 'H' ? jalview.renderer.AnnotationRenderer.HELIX_COLOUR
+                          : annotation.annotations[j].secondaryStructure == 'E' ? jalview.renderer.AnnotationRenderer.SHEET_COLOUR
+                                  : jalview.renderer.AnnotationRenderer.STEM_COLOUR;
+                }
+              }
+            }
+            else
+            {
+              //
+              return Color.white;
+            }
+          }
+          else if (noGradient)
+          {
+            if (colourScheme != null)
+            {
+              currentColour = colourScheme.findColour(c, j, seq);
+            }
+            else
+            {
+              if (aj.colour != null)
+              {
+                currentColour = aj.colour;
+              }
+            }
+          }
+          else
+          {
+            currentColour = shadeCalculation(annotation, j);
+          }
+        }
+        if (conservationColouring)
+        {
+          currentColour = applyConservation(currentColour, j);
+        }
+      }
+    }
+    return currentColour;
+  }
+
+  private Color shadeCalculation(AlignmentAnnotation annotation, int j)
+  {
+
+    // calculate a shade
+    float range = 1f;
+    if (thresholdIsMinMax
+            && annotation.threshold != null
+            && aboveAnnotationThreshold == ABOVE_THRESHOLD
+            && annotation.annotations[j].value >= annotation.threshold.value)
+    {
+      range = (annotation.annotations[j].value - annotation.threshold.value)
+              / (annotation.graphMax - annotation.threshold.value);
+    }
+    else if (thresholdIsMinMax && annotation.threshold != null
+            && aboveAnnotationThreshold == BELOW_THRESHOLD
+            && annotation.annotations[j].value >= annotation.graphMin)
+    {
+      range = (annotation.annotations[j].value - annotation.graphMin)
+              / (annotation.threshold.value - annotation.graphMin);
+    }
+    else
+    {
+      if (annotation.graphMax != annotation.graphMin)
+      {
+        range = (annotation.annotations[j].value - annotation.graphMin)
+                / (annotation.graphMax - annotation.graphMin);
+      }
+      else
+      {
+        range = 0f;
+      }
+    }
+
+    int dr = (int) (rr * range + r1), dg = (int) (gg * range + g1), db = (int) (bb
+            * range + b1);
+
+    return new Color(dr, dg, db);
+
+  }
+  public boolean isPredefinedColours()
+  {
+    return predefinedColours;
+  }
+
+  public void setPredefinedColours(boolean predefinedColours)
+  {
+    this.predefinedColours = predefinedColours;
+  }
+
+  public boolean isSeqAssociated()
+  {
+    return seqAssociated;
+  }
+
+  public void setSeqAssociated(boolean sassoc)
+  {
+    seqAssociated = sassoc;
+  }
+}