-/*\r
-* Jalview - A Sequence Alignment Editor and Viewer\r
-* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
-*\r
-* This program is free software; you can redistribute it and/or\r
-* modify it under the terms of the GNU General Public License\r
-* as published by the Free Software Foundation; either version 2\r
-* of the License, or (at your option) any later version.\r
-*\r
-* This program is distributed in the hope that it will be useful,\r
-* but WITHOUT ANY WARRANTY; without even the implied warranty of\r
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
-* GNU General Public License for more details.\r
-*\r
-* You should have received a copy of the GNU General Public License\r
-* along with this program; if not, write to the Free Software\r
-* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
-*/\r
-package jalview.schemes;\r
-\r
-import java.awt.*;\r
-\r
-import jalview.datamodel.*;\r
-\r
-public class AnnotationColourGradient extends ResidueColourScheme\r
-{\r
- public static int NO_THRESHOLD = -1;\r
- public static int BELOW_THRESHOLD = 0;\r
- public static int ABOVE_THRESHOLD = 1;\r
-\r
- AlignmentAnnotation annotation;\r
- int aboveAnnotationThreshold = -1;\r
-\r
- GraphLine annotationThreshold;\r
-\r
- float r1, g1, b1, rr, gg, bb, dr, dg, db;\r
- float range = 0;\r
-\r
- ColourSchemeI colourScheme;\r
-\r
- /**\r
- * Creates a new AnnotationColourGradient object.\r
- */\r
- public AnnotationColourGradient(AlignmentAnnotation annotation,\r
- ColourSchemeI originalColour,\r
- int aboveThreshold)\r
- {\r
- if(originalColour instanceof AnnotationColourGradient)\r
- {\r
- colourScheme = ((AnnotationColourGradient)originalColour).colourScheme;\r
- }\r
- else\r
- colourScheme = originalColour;\r
-\r
- this.annotation = annotation;\r
-\r
- aboveAnnotationThreshold = aboveThreshold;\r
-\r
- if(aboveThreshold!=NO_THRESHOLD && annotation.threshold!=null)\r
- annotationThreshold = annotation.threshold;\r
- }\r
-\r
- /**\r
- * Creates a new AnnotationColourGradient object.\r
- */\r
- public AnnotationColourGradient(AlignmentAnnotation annotation,\r
- Color minColour, Color maxColour, int aboveThreshold)\r
- {\r
- this.annotation = annotation;\r
-\r
- aboveAnnotationThreshold = aboveThreshold;\r
-\r
- if(aboveThreshold!=NO_THRESHOLD && annotation.threshold!=null)\r
- annotationThreshold = annotation.threshold;\r
-\r
- r1 = minColour.getRed();\r
- g1 = minColour.getGreen();\r
- b1 = minColour.getBlue();\r
-\r
- rr = maxColour.getRed() - r1;\r
- gg = maxColour.getGreen() - g1;\r
- bb = maxColour.getBlue() - b1;\r
-\r
- range = annotation.graphMax - annotation.graphMin;\r
-\r
- }\r
-\r
-\r
- public String getAnnotation()\r
- {\r
- return annotation.label;\r
- }\r
-\r
- public int getAboveThreshold()\r
- {\r
- return aboveAnnotationThreshold;\r
- }\r
-\r
- public float getAnnotationThreshold()\r
- {\r
- if(annotationThreshold==null)\r
- return 0;\r
- else\r
- return annotationThreshold.value;\r
- }\r
-\r
- public ColourSchemeI getBaseColour()\r
- {\r
- return colourScheme;\r
- }\r
-\r
- public Color getMinColour()\r
- {\r
- return new Color( (int) r1, (int) g1, (int) b1);\r
- }\r
-\r
- public Color getMaxColour()\r
- {\r
- return new Color( (int) (r1 + rr), (int) (g1 + gg), (int) (b1 + bb));\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param n DOCUMENT ME!\r
- *\r
- * @return DOCUMENT ME!\r
- */\r
- public Color findColour(String n)\r
- {\r
- return Color.red;\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param n DOCUMENT ME!\r
- * @param j DOCUMENT ME!\r
- *\r
- * @return DOCUMENT ME!\r
- */\r
- public Color findColour(String n, int j)\r
- {\r
- currentColour = Color.white;\r
-\r
- if ((threshold == 0) || aboveThreshold(n, j))\r
- {\r
- if( j<annotation.annotations.length\r
- && annotation.annotations[j]!=null\r
- && !jalview.util.Comparison.isGap(n.charAt(0)))\r
- {\r
- if( aboveAnnotationThreshold==NO_THRESHOLD\r
- || (annotationThreshold!=null && aboveAnnotationThreshold==ABOVE_THRESHOLD && annotation.annotations[j].value>=annotationThreshold.value)\r
- || (annotationThreshold!=null && aboveAnnotationThreshold==BELOW_THRESHOLD && annotation.annotations[j].value<=annotationThreshold.value))\r
- {\r
- if(colourScheme!=null)\r
- {\r
- currentColour = colourScheme.findColour(n, j);\r
- }\r
- else if(range!=0)\r
- {\r
- dr = rr *\r
- ( (annotation.annotations[j].value - annotation.graphMin) /\r
- range)\r
- + r1;\r
- dg = gg *\r
- ( (annotation.annotations[j].value - annotation.graphMin) /\r
- range)\r
- + g1;\r
- db = bb *\r
- ( (annotation.annotations[j].value - annotation.graphMin) /\r
- range)\r
- + b1;\r
-\r
- currentColour = new Color( (int) dr, (int) dg, (int) db);\r
- }\r
- }\r
- }\r
- }\r
-\r
- if(conservationColouring)\r
- applyConservation(j);\r
-\r
- return currentColour;\r
- }\r
-}\r
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ *
+ * 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/>.
+ */
+package jalview.schemes;
+
+import java.awt.*;
+
+import jalview.datamodel.*;
+
+public class AnnotationColourGradient extends ResidueColourScheme
+{
+ 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, dr, dg, db;
+
+ ColourSchemeI colourScheme;
+
+ public boolean predefinedColours = false;
+
+ /**
+ * 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;
+ }
+ }
+
+ /**
+ * 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;
+ }
+
+ public String getAnnotation()
+ {
+ return annotation.label;
+ }
+
+ public int getAboveThreshold()
+ {
+ return aboveAnnotationThreshold;
+ }
+
+ public float getAnnotationThreshold()
+ {
+ if (annotationThreshold == null)
+ {
+ return 0;
+ }
+ else
+ {
+ return annotationThreshold.value;
+ }
+ }
+
+ public ColourSchemeI getBaseColour()
+ {
+ return colourScheme;
+ }
+
+ 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!
+ */
+ public Color findColour(char c, int j)
+ {
+ Color currentColour = Color.white;
+
+ if ((threshold == 0) || aboveThreshold(c, j))
+ {
+ if (j < annotation.annotations.length
+ && annotation.annotations[j] != null
+ && !jalview.util.Comparison.isGap(c))
+ {
+
+ if (predefinedColours)
+ {
+ if (annotation.annotations[j].colour != null)
+ return annotation.annotations[j].colour;
+ else
+ return currentColour;
+ }
+
+ if (aboveAnnotationThreshold == NO_THRESHOLD
+ || (annotationThreshold != null
+ && aboveAnnotationThreshold == ABOVE_THRESHOLD && annotation.annotations[j].value >= annotationThreshold.value)
+ || (annotationThreshold != null
+ && aboveAnnotationThreshold == BELOW_THRESHOLD && annotation.annotations[j].value <= annotationThreshold.value))
+ {
+
+ 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
+ {
+ range = (annotation.annotations[j].value - annotation.graphMin)
+ / (annotation.graphMax - annotation.graphMin);
+ }
+
+ if (colourScheme != null)
+ {
+ currentColour = colourScheme.findColour(c, j);
+ }
+ else if (range != 0)
+ {
+ dr = rr * range + r1;
+ dg = gg * range + g1;
+ db = bb * range + b1;
+
+ currentColour = new Color((int) dr, (int) dg, (int) db);
+ }
+ }
+ }
+ }
+
+ if (conservationColouring)
+ {
+ currentColour = applyConservation(currentColour, j);
+ }
+
+ return currentColour;
+ }
+}
git://source.jalview.org / jalview.git / blobdiff