X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FUserColourScheme.java;h=89f3eed3a72e8ac78599640ec1897704e75fae7e;hb=17e77c3f2949a0729322b4a8d907f3f34b6a9914;hp=9d61279ffdf679deb1643f7b6f2c9ad6b0aa8aa7;hpb=3d941a02a998676a12f8ff43fa98d9e1f4c27142;p=jalview.git
diff --git a/src/jalview/schemes/UserColourScheme.java b/src/jalview/schemes/UserColourScheme.java
index 9d61279..89f3eed 100755
--- a/src/jalview/schemes/UserColourScheme.java
+++ b/src/jalview/schemes/UserColourScheme.java
@@ -1,218 +1,266 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2006 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 java.util.StringTokenizer;
-
-public class UserColourScheme
- extends ResidueColourScheme
-{
- Color [] lowerCaseColours;
-
- protected String schemeName;
-
- public UserColourScheme()
- { }
-
- public UserColourScheme(Color[] newColors)
- {
- colors = newColors;
- }
-
- public UserColourScheme(String colour)
- {
- Color col = getColourFromString(colour);
-
- if(col==null)
- {
- System.out.println("Unknown colour!! "+colour);
- col = createColourFromName(colour);
- }
-
- colors = new Color[24];
- for(int i=0; i<24; i++)
- colors[i] = col;
- }
-
- public Color[] getColours()
- {
- return colors;
- }
-
- public Color[] getLowerCaseColours()
- {
- return lowerCaseColours;
- }
-
- public void setName(String name)
- {
- schemeName = name;
- }
-
- public String getName()
- {
- return schemeName;
- }
-
- public Color getColourFromString(String colour)
- {
- colour = colour.trim();
-
- Color col = null;
- try
- {
- int value = Integer.parseInt(colour, 16);
- col = new Color(value);
- }
- catch (NumberFormatException ex)
- {}
-
- if (col == null)
- col = ColourSchemeProperty.getAWTColorFromName(colour);
-
- if (col == null)
- {
- try
- {
- java.util.StringTokenizer st = new java.util.StringTokenizer(colour,
- ",");
- int r = Integer.parseInt(st.nextToken());
- int g = Integer.parseInt(st.nextToken());
- int b = Integer.parseInt(st.nextToken());
- col = new Color(r, g, b);
- }
- catch (Exception ex)
- {}
- }
-
- return col;
-
- }
-
- public Color createColourFromName(String name)
- {
- int r, g, b;
-
- int lsize = name.length();
- int start = 0, end = lsize / 3;
-
- int rgbOffset = Math.abs(name.hashCode() % 10) * 15;
-
- r = Math.abs(name.substring(start, end).hashCode() + rgbOffset) % 210 + 20;
- start = end;
- end += lsize / 3;
- if (end > lsize)
- end = lsize;
-
- g = Math.abs(name.substring(start, end).hashCode() + rgbOffset) % 210 + 20;
-
- b = Math.abs(name.substring(end).hashCode() + rgbOffset) % 210 + 20;
-
- Color color = new Color(r, g, b);
-
- return color;
- }
-
- public void parseAppletParameter(String paramValue)
- {
- StringTokenizer st = new StringTokenizer(paramValue, ";");
- StringTokenizer st2;
- String token=null, colour, residues;
- try{
- while (st.hasMoreElements())
- {
- token = st.nextToken().trim();
- residues = token.substring(0, token.indexOf("="));
- colour = token.substring(token.indexOf("=") + 1);
-
- st2 = new StringTokenizer(residues, " ,");
- while (st2.hasMoreTokens())
- {
- token = st2.nextToken();
-
- if (ResidueProperties.aaIndex[token.charAt(0)]==-1)
- continue;
-
- int colIndex = ResidueProperties.aaIndex[token.charAt(0)];
-
- if(token.equalsIgnoreCase("lowerCase"))
- {
- if (lowerCaseColours == null)
- lowerCaseColours = new Color[23];
- for (int i = 0; i < 23; i++)
- if (lowerCaseColours[i] == null)
- lowerCaseColours[i] = getColourFromString(colour);
-
- continue;
- }
-
- if(token.equals(token.toLowerCase()))
- {
- if(lowerCaseColours==null)
- {
- lowerCaseColours = new Color[23];
- }
- lowerCaseColours[colIndex] = getColourFromString(colour);
- }
- else
- colors[colIndex] = getColourFromString(colour);
- }
- }
- }
- catch(Exception ex)
- {
- System.out.println("Error parsing userDefinedColours:\n"
- +token+"\n"+ex);
- }
-
- }
-
-
-
- public Color findColour(String s, int j)
- {
- Color currentColour;
- int index = ResidueProperties.aaIndex[s.charAt(0)];
-
- if ((threshold == 0) || aboveThreshold(ResidueProperties.aa[index], j))
- {
- if(lowerCaseColours!=null && 'a' <= s.charAt(0) && s.charAt(0) <= 'z')
- currentColour = lowerCaseColours[index];
- else
- currentColour = colors[index];
- }
- else
- {
- currentColour = Color.white;
- }
-
- if(conservationColouring)
- applyConservation(currentColour, j);
-
-
- return currentColour;
- }
-
- public void setLowerCaseColours(Color [] lcolours)
- {
- lowerCaseColours = lcolours;
- }
-
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 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 .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.schemes;
+
+import jalview.datamodel.AnnotatedCollectionI;
+import jalview.datamodel.SequenceCollectionI;
+import jalview.datamodel.SequenceI;
+
+import java.awt.Color;
+import java.util.Map;
+import java.util.StringTokenizer;
+
+public class UserColourScheme extends ResidueColourScheme
+{
+ Color[] lowerCaseColours;
+
+ protected String schemeName;
+
+ public UserColourScheme()
+ {
+ super(ResidueProperties.aaIndex);
+ }
+
+ public UserColourScheme(Color[] newColors)
+ {
+ super(ResidueProperties.aaIndex);
+ colors = newColors;
+ }
+
+ @Override
+ public ColourSchemeI applyTo(AnnotatedCollectionI sg,
+ Map hiddenRepSequences)
+ {
+ UserColourScheme usc = new UserColourScheme(colors);
+ if (lowerCaseColours != null)
+ {
+ usc.schemeName = new String(schemeName);
+ usc.lowerCaseColours = new Color[lowerCaseColours.length];
+ System.arraycopy(lowerCaseColours, 0, usc.lowerCaseColours, 0,
+ lowerCaseColours.length);
+ }
+ return usc;
+ }
+
+ public UserColourScheme(String colour)
+ {
+ super(ResidueProperties.aaIndex);
+ Color col = getColourFromString(colour);
+
+ if (col == null)
+ {
+ System.out.println("Unknown colour!! " + colour);
+ col = createColourFromName(colour);
+ }
+
+ colors = new Color[24];
+ for (int i = 0; i < 24; i++)
+ {
+ colors[i] = col;
+ }
+ schemeName = colour;
+ }
+
+ public Color[] getColours()
+ {
+ return colors;
+ }
+
+ public Color[] getLowerCaseColours()
+ {
+ return lowerCaseColours;
+ }
+
+ public void setName(String name)
+ {
+ schemeName = name;
+ }
+
+ public String getName()
+ {
+ return schemeName;
+ }
+
+ public Color getColourFromString(String colour)
+ {
+ colour = colour.trim();
+
+ Color col = null;
+ try
+ {
+ int value = Integer.parseInt(colour, 16);
+ col = new Color(value);
+ } catch (NumberFormatException ex)
+ {
+ }
+
+ if (col == null)
+ {
+ col = ColourSchemeProperty.getAWTColorFromName(colour);
+ }
+
+ if (col == null)
+ {
+ try
+ {
+ java.util.StringTokenizer st = new java.util.StringTokenizer(
+ colour, ",");
+ int r = Integer.parseInt(st.nextToken());
+ int g = Integer.parseInt(st.nextToken());
+ int b = Integer.parseInt(st.nextToken());
+ col = new Color(r, g, b);
+ } catch (Exception ex)
+ {
+ }
+ }
+
+ return col;
+
+ }
+
+ public Color createColourFromName(String name)
+ {
+ int r, g, b;
+
+ int lsize = name.length();
+ int start = 0, end = lsize / 3;
+
+ int rgbOffset = Math.abs(name.hashCode() % 10) * 15;
+
+ r = Math.abs(name.substring(start, end).hashCode() + rgbOffset) % 210 + 20;
+ start = end;
+ end += lsize / 3;
+ if (end > lsize)
+ {
+ end = lsize;
+ }
+
+ g = Math.abs(name.substring(start, end).hashCode() + rgbOffset) % 210 + 20;
+
+ b = Math.abs(name.substring(end).hashCode() + rgbOffset) % 210 + 20;
+
+ Color color = new Color(r, g, b);
+
+ return color;
+ }
+
+ public void parseAppletParameter(String paramValue)
+ {
+ // TODO: need a function to generate appletParameter colour string from a
+ // UCS
+ StringTokenizer st = new StringTokenizer(paramValue, ";");
+ StringTokenizer st2;
+ String token = null, colour, residues;
+ try
+ {
+ while (st.hasMoreElements())
+ {
+ token = st.nextToken().trim();
+ residues = token.substring(0, token.indexOf("="));
+ colour = token.substring(token.indexOf("=") + 1);
+
+ st2 = new StringTokenizer(residues, " ,");
+ while (st2.hasMoreTokens())
+ {
+ token = st2.nextToken();
+
+ if (ResidueProperties.aaIndex[token.charAt(0)] == -1)
+ {
+ continue;
+ }
+
+ int colIndex = ResidueProperties.aaIndex[token.charAt(0)];
+
+ if (token.equalsIgnoreCase("lowerCase"))
+ {
+ if (lowerCaseColours == null)
+ {
+ lowerCaseColours = new Color[23];
+ }
+ for (int i = 0; i < 23; i++)
+ {
+ if (lowerCaseColours[i] == null)
+ {
+ lowerCaseColours[i] = getColourFromString(colour);
+ }
+ }
+
+ continue;
+ }
+
+ if (token.equals(token.toLowerCase()))
+ {
+ if (lowerCaseColours == null)
+ {
+ lowerCaseColours = new Color[23];
+ }
+ lowerCaseColours[colIndex] = getColourFromString(colour);
+ }
+ else
+ {
+ colors[colIndex] = getColourFromString(colour);
+ }
+ }
+ }
+ } catch (Exception ex)
+ {
+ System.out.println("Error parsing userDefinedColours:\n" + token
+ + "\n" + ex);
+ }
+
+ }
+
+ @Override
+ public Color findColour(char c, int j, SequenceI seq)
+ {
+ Color currentColour;
+ int index = ResidueProperties.aaIndex[c];
+
+ if ((threshold == 0) || aboveThreshold(c, j))
+ {
+ if (lowerCaseColours != null && 'a' <= c && c <= 'z')
+ {
+ currentColour = lowerCaseColours[index];
+ }
+ else
+ {
+ currentColour = colors[index];
+ }
+ }
+ else
+ {
+ currentColour = Color.white;
+ }
+
+ if (conservationColouring)
+ {
+ currentColour = applyConservation(currentColour, j);
+ }
+
+ return currentColour;
+ }
+
+ public void setLowerCaseColours(Color[] lcolours)
+ {
+ lowerCaseColours = lcolours;
+ }
+
+}