X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FColourSchemeProperty.java;h=d27dcf012972f2a43fd081f4a29e20748803ec61;hb=efc31b4a8d5cee63555586804a2b79c06bdb5a14;hp=0d5ecc7b1478aff8a9a6bd1f56edcef8efa938d6;hpb=9257b8510c7354cbd7e43a3fc2817978cc8e4ae9;p=jalview.git

diff --git a/src/jalview/schemes/ColourSchemeProperty.java b/src/jalview/schemes/ColourSchemeProperty.java
index 0d5ecc7..d27dcf0 100755
--- a/src/jalview/schemes/ColourSchemeProperty.java
+++ b/src/jalview/schemes/ColourSchemeProperty.java
@@ -18,88 +18,187 @@
 */
 package jalview.schemes;
 
-public class ColourSchemeProperty {
+import java.awt.*;
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class ColourSchemeProperty
+{
+    /** DOCUMENT ME!! */
     public static final int CLUSTAL = 0;
+
+    /** DOCUMENT ME!! */
     public static final int BLOSUM = 1;
+
+    /** DOCUMENT ME!! */
     public static final int PID = 2;
+
+    /** DOCUMENT ME!! */
     public static final int ZAPPO = 3;
+
+    /** DOCUMENT ME!! */
     public static final int HYDROPHOBIC = 4;
+
+    /** DOCUMENT ME!! */
     public static final int HELIX = 5;
+
+    /** DOCUMENT ME!! */
     public static final int STRAND = 6;
+
+    /** DOCUMENT ME!! */
     public static final int TURN = 7;
+
+    /** DOCUMENT ME!! */
     public static final int BURIED = 8;
+
+    /** DOCUMENT ME!! */
     public static final int NUCLEOTIDE = 9;
+
+    /** DOCUMENT ME!! */
     public static final int USER_DEFINED = 10;
+
+    /** DOCUMENT ME!! */
     public static final int NONE = 11;
 
-    public static int getColourIndexFromName(String name) {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param name DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public static int getColourIndexFromName(String name)
+    {
         int ret = 11;
 
-        if (name.equalsIgnoreCase("Clustal")) {
+        if (name.equalsIgnoreCase("Clustal"))
+        {
             ret = CLUSTAL;
-        } else if (name.equalsIgnoreCase("Blosum62")) {
+        }
+        else if (name.equalsIgnoreCase("Blosum62"))
+        {
             ret = BLOSUM;
-        } else if (name.equalsIgnoreCase("% Identity")) {
+        }
+        else if (name.equalsIgnoreCase("% Identity"))
+        {
             ret = PID;
-        } else if (name.equalsIgnoreCase("Zappo")) {
+        }
+        else if (name.equalsIgnoreCase("Zappo"))
+        {
             ret = ZAPPO;
-        } else if (name.equalsIgnoreCase("Hydrophobic")) {
+        }
+        else if (name.equalsIgnoreCase("Hydrophobic"))
+        {
             ret = HYDROPHOBIC;
-        } else if (name.equalsIgnoreCase("Helix Propensity")) {
+        }
+        else if (name.equalsIgnoreCase("Helix Propensity"))
+        {
             ret = HELIX;
-        } else if (name.equalsIgnoreCase("Strand Propensity")) {
+        }
+        else if (name.equalsIgnoreCase("Strand Propensity"))
+        {
             ret = STRAND;
-        } else if (name.equalsIgnoreCase("Turn Propensity")) {
+        }
+        else if (name.equalsIgnoreCase("Turn Propensity"))
+        {
             ret = TURN;
-        } else if (name.equalsIgnoreCase("Buried Index")) {
+        }
+        else if (name.equalsIgnoreCase("Buried Index"))
+        {
             ret = BURIED;
-        } else if (name.equalsIgnoreCase("Nucleotide")) {
+        }
+        else if (name.equalsIgnoreCase("Nucleotide"))
+        {
             ret = NUCLEOTIDE;
-        } else if (name.equalsIgnoreCase("User Defined")) {
+        }
+        else if (name.equalsIgnoreCase("User Defined"))
+        {
             ret = USER_DEFINED;
         }
 
         return ret;
     }
 
-    public static String getColourName(ColourSchemeI cs) {
-        if (cs instanceof ConservationColourScheme) {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param cs DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public static String getColourName(ColourSchemeI cs)
+    {
+        if (cs instanceof ConservationColourScheme)
+        {
             cs = ((ConservationColourScheme) cs).cs;
         }
 
         int index = 11;
 
-        if (cs instanceof ClustalxColourScheme) {
+        if (cs instanceof ClustalxColourScheme)
+        {
             index = CLUSTAL;
-        } else if (cs instanceof Blosum62ColourScheme) {
+        }
+        else if (cs instanceof Blosum62ColourScheme)
+        {
             index = BLOSUM;
-        } else if (cs instanceof PIDColourScheme) {
+        }
+        else if (cs instanceof PIDColourScheme)
+        {
             index = PID;
-        } else if (cs instanceof ZappoColourScheme) {
+        }
+        else if (cs instanceof ZappoColourScheme)
+        {
             index = ZAPPO;
-        } else if (cs instanceof HydrophobicColourScheme) {
+        }
+        else if (cs instanceof HydrophobicColourScheme)
+        {
             index = HYDROPHOBIC;
-        } else if (cs instanceof HelixColourScheme) {
+        }
+        else if (cs instanceof HelixColourScheme)
+        {
             index = HELIX;
-        } else if (cs instanceof StrandColourScheme) {
+        }
+        else if (cs instanceof StrandColourScheme)
+        {
             index = STRAND;
-        } else if (cs instanceof TurnColourScheme) {
+        }
+        else if (cs instanceof TurnColourScheme)
+        {
             index = TURN;
-        } else if (cs instanceof BuriedColourScheme) {
+        }
+        else if (cs instanceof BuriedColourScheme)
+        {
             index = BURIED;
-        } else if (cs instanceof NucleotideColourScheme) {
+        }
+        else if (cs instanceof NucleotideColourScheme)
+        {
             index = NUCLEOTIDE;
-        } else if (cs instanceof UserColourScheme) {
+        }
+        else if (cs instanceof UserColourScheme)
+        {
             index = USER_DEFINED;
         }
 
         return getColourName(index);
     }
 
-    public static String getColourName(int index) {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param index DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public static String getColourName(int index)
+    {
         String ret = null;
 
-        switch (index) {
+        switch (index)
+        {
         case CLUSTAL:
             ret = "Clustal";
 
@@ -164,21 +263,51 @@ public class ColourSchemeProperty {
         return ret;
     }
 
-    public static ColourSchemeI getColour(jalview.datamodel.AlignmentI al, String name)
+    /**
+     * DOCUMENT ME!
+     *
+     * @param al DOCUMENT ME!
+     * @param name DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public static ColourSchemeI getColour(jalview.datamodel.AlignmentI al,
+        String name)
     {
-     return getColour(al.getSequences(), al.getWidth(), name);
+        return getColour(al.getSequences(), al.getWidth(), name);
     }
 
+    /**
+     * DOCUMENT ME!
+     *
+     * @param seqs DOCUMENT ME!
+     * @param width DOCUMENT ME!
+     * @param name DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
     public static ColourSchemeI getColour(java.util.Vector seqs, int width,
-        String name) {
+        String name)
+    {
         return getColour(seqs, width, getColourIndexFromName(name));
     }
 
+    /**
+     * DOCUMENT ME!
+     *
+     * @param seqs DOCUMENT ME!
+     * @param width DOCUMENT ME!
+     * @param index DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
     public static ColourSchemeI getColour(java.util.Vector seqs, int width,
-        int index) {
+        int index)
+    {
         ColourSchemeI cs = null;
 
-        switch (index) {
+        switch (index)
+        {
         case CLUSTAL:
             cs = new ClustalxColourScheme(seqs, width);
 
@@ -230,7 +359,7 @@ public class ColourSchemeProperty {
             break;
 
         case USER_DEFINED:
-            cs = new UserColourScheme(null);
+            cs = new UserColourScheme(new Color[0]);
 
             break;
 
@@ -240,4 +369,38 @@ public class ColourSchemeProperty {
 
         return cs;
     }
+
+    public static Color getAWTColorFromName(String name)
+    {
+      Color col = null;
+      name = name.toLowerCase();
+      if(name.equals("black"))
+        col = Color.black;
+      else if(name.equals("blue"))
+        col = Color.blue;
+      else if(name.equals("cyan"))
+        col = Color.cyan;
+      else if(name.equals("darkGray"))
+        col = Color.darkGray;
+      else if(name.equals("gray"))
+        col = Color.gray;
+      else if(name.equals("green"))
+        col = Color.green;
+      else if(name.equals("lightGray"))
+        col = Color.lightGray;
+      else if(name.equals("magenta"))
+        col = Color.magenta;
+      else if(name.equals("orange"))
+        col = Color.orange;
+      else if(name.equals("pink"))
+        col = Color.pink;
+      else if(name.equals("red"))
+        col = Color.red;
+      else if(name.equals("white"))
+        col = Color.white;
+      else if(name.equals("yellow"))
+        col = Color.yellow;
+
+      return col;
+    }
 }