X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FColourSchemeProperty.java;h=d27dcf012972f2a43fd081f4a29e20748803ec61;hb=b59132cb08bb83359dd7fcb17c50a964d4b162c5;hp=a9815492748a8e1c51c541d5bcfcaddcdea299e6;hpb=99c58ee0ae2a848f982552e53feaf6d5cb9925e5;p=jalview.git

diff --git a/src/jalview/schemes/ColourSchemeProperty.java b/src/jalview/schemes/ColourSchemeProperty.java
index a981549..d27dcf0 100755
--- a/src/jalview/schemes/ColourSchemeProperty.java
+++ b/src/jalview/schemes/ColourSchemeProperty.java
@@ -16,133 +16,391 @@
 * 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.*;
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
 public class ColourSchemeProperty
 {
-  public static final int CLUSTAL = 0;
-  public static final int BLOSUM = 1;
-  public static final int PID = 2;
-  public static final int ZAPPO = 3;
-  public static final int HYDROPHOBIC=4;
-  public static final int HELIX=5;
-  public static final int STRAND=6;
-  public static final int TURN = 7;
-  public static final int BURIED = 8;
-  public static final int NUCLEOTIDE = 9;
-  public static final int USER_DEFINED = 10;
-  public static final int NONE = 11;
-
-  public static int getColourIndexFromName(String name)
-  {
-    int ret=11;
-    if(name.equalsIgnoreCase("Clustal"))
-      ret = CLUSTAL;
-    else if(name.equalsIgnoreCase("Blosum62"))
-      ret = BLOSUM;
-    else if(name.equalsIgnoreCase("% Identity"))
-      ret = PID;
-    else if(name.equalsIgnoreCase("Zappo"))
-      ret = ZAPPO;
-    else if(name.equalsIgnoreCase("Hydrophobic"))
-      ret = HYDROPHOBIC;
-    else if(name.equalsIgnoreCase("Helix Propensity"))
-      ret = HELIX;
-    else if(name.equalsIgnoreCase("Strand Propensity"))
-      ret = STRAND;
-    else if(name.equalsIgnoreCase("Turn Propensity"))
-      ret = TURN;
-    else if(name.equalsIgnoreCase("Buried Index"))
-      ret = BURIED;
-    else if(name.equalsIgnoreCase("Nucleotide"))
-      ret = NUCLEOTIDE;
-    else if(name.equalsIgnoreCase("User Defined"))
-      ret =  USER_DEFINED;
-
-    return ret;
-  }
-
-  public static String getColourName(ColourSchemeI cs)
-  {
-    if(cs instanceof ConservationColourScheme)
-     cs = ((ConservationColourScheme)cs).cs;
-
-
-    int index = 11;
-    if(cs instanceof ClustalxColourScheme)
-      index = CLUSTAL;
-    else if(cs instanceof  Blosum62ColourScheme)
-      index = BLOSUM;
-    else if(cs instanceof  PIDColourScheme)
-      index = PID;
-    else if(cs instanceof  ZappoColourScheme)
-      index = ZAPPO;
-    else if(cs instanceof  HydrophobicColourScheme)
-      index = HYDROPHOBIC;
-    else if(cs instanceof  HelixColourScheme)
-      index = HELIX;
-    else if(cs instanceof  StrandColourScheme)
-      index = STRAND;
-    else if(cs instanceof  TurnColourScheme)
-      index = TURN;
-    else if(cs instanceof  BuriedColourScheme)
-      index = BURIED;
-    else if(cs instanceof  NucleotideColourScheme)
-      index = NUCLEOTIDE;
-    else if(cs instanceof  UserColourScheme)
-      index = USER_DEFINED;
-
-    return getColourName(index);
-  }
-
-  public static String getColourName(int index)
-  {
-    String ret=null;
-    switch(index)
+    /** 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;
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param name DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public static int getColourIndexFromName(String name)
     {
-      case CLUSTAL: ret = "Clustal";    break;
-      case BLOSUM:  ret = "Blosum62";   break;
-      case PID:     ret = "% Identity"; break;
-      case ZAPPO:   ret = "Zappo";      break;
-      case HYDROPHOBIC: ret="Hydrophobic";break;
-      case HELIX:   ret="Helix Propensity";break;
-      case STRAND:  ret="Strand Propensity";break;
-      case TURN:    ret="Turn Propensity";break;
-      case BURIED:  ret="Buried Index";break;
-      case NUCLEOTIDE:ret="Nucleotide"; break;
-      case USER_DEFINED:ret="User Defined";break;
-      default: ret = "None"; break;
+        int ret = 11;
+
+        if (name.equalsIgnoreCase("Clustal"))
+        {
+            ret = CLUSTAL;
+        }
+        else if (name.equalsIgnoreCase("Blosum62"))
+        {
+            ret = BLOSUM;
+        }
+        else if (name.equalsIgnoreCase("% Identity"))
+        {
+            ret = PID;
+        }
+        else if (name.equalsIgnoreCase("Zappo"))
+        {
+            ret = ZAPPO;
+        }
+        else if (name.equalsIgnoreCase("Hydrophobic"))
+        {
+            ret = HYDROPHOBIC;
+        }
+        else if (name.equalsIgnoreCase("Helix Propensity"))
+        {
+            ret = HELIX;
+        }
+        else if (name.equalsIgnoreCase("Strand Propensity"))
+        {
+            ret = STRAND;
+        }
+        else if (name.equalsIgnoreCase("Turn Propensity"))
+        {
+            ret = TURN;
+        }
+        else if (name.equalsIgnoreCase("Buried Index"))
+        {
+            ret = BURIED;
+        }
+        else if (name.equalsIgnoreCase("Nucleotide"))
+        {
+            ret = NUCLEOTIDE;
+        }
+        else if (name.equalsIgnoreCase("User Defined"))
+        {
+            ret = USER_DEFINED;
+        }
+
+        return ret;
     }
-    return ret;
-  }
-
-  public static ColourSchemeI getColour(jalview.datamodel.AlignmentI al, String name)
-  {
-    return getColour(al, getColourIndexFromName(name));
-  }
-
-  public static ColourSchemeI getColour(jalview.datamodel.AlignmentI al, int index)
-  {
-    ColourSchemeI cs = null;
-    switch(index)
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param cs DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public static String getColourName(ColourSchemeI cs)
     {
-      case CLUSTAL: cs = new ClustalxColourScheme(al.getSequences(), al.getWidth()); break;
-      case BLOSUM: cs = new Blosum62ColourScheme(); break;
-      case PID: cs = new PIDColourScheme();  break;
-      case ZAPPO: cs = new ZappoColourScheme(); break;
-      case HYDROPHOBIC: cs = new HydrophobicColourScheme(); break;
-      case HELIX: cs = new HelixColourScheme(); break;
-      case STRAND: cs = new StrandColourScheme(); break;
-      case TURN: cs = new TurnColourScheme(); break;
-      case BURIED: cs = new BuriedColourScheme(); break;
-      case NUCLEOTIDE: cs = new NucleotideColourScheme(); break;
-      case USER_DEFINED: cs = new UserColourScheme(null);
-        break;
-
-      default: break;
+        if (cs instanceof ConservationColourScheme)
+        {
+            cs = ((ConservationColourScheme) cs).cs;
+        }
+
+        int index = 11;
+
+        if (cs instanceof ClustalxColourScheme)
+        {
+            index = CLUSTAL;
+        }
+        else if (cs instanceof Blosum62ColourScheme)
+        {
+            index = BLOSUM;
+        }
+        else if (cs instanceof PIDColourScheme)
+        {
+            index = PID;
+        }
+        else if (cs instanceof ZappoColourScheme)
+        {
+            index = ZAPPO;
+        }
+        else if (cs instanceof HydrophobicColourScheme)
+        {
+            index = HYDROPHOBIC;
+        }
+        else if (cs instanceof HelixColourScheme)
+        {
+            index = HELIX;
+        }
+        else if (cs instanceof StrandColourScheme)
+        {
+            index = STRAND;
+        }
+        else if (cs instanceof TurnColourScheme)
+        {
+            index = TURN;
+        }
+        else if (cs instanceof BuriedColourScheme)
+        {
+            index = BURIED;
+        }
+        else if (cs instanceof NucleotideColourScheme)
+        {
+            index = NUCLEOTIDE;
+        }
+        else if (cs instanceof UserColourScheme)
+        {
+            index = USER_DEFINED;
+        }
+
+        return getColourName(index);
     }
 
-    return cs;
-  }
+    /**
+     * DOCUMENT ME!
+     *
+     * @param index DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public static String getColourName(int index)
+    {
+        String ret = null;
+
+        switch (index)
+        {
+        case CLUSTAL:
+            ret = "Clustal";
+
+            break;
+
+        case BLOSUM:
+            ret = "Blosum62";
+
+            break;
+
+        case PID:
+            ret = "% Identity";
+
+            break;
+
+        case ZAPPO:
+            ret = "Zappo";
+
+            break;
+
+        case HYDROPHOBIC:
+            ret = "Hydrophobic";
+
+            break;
+
+        case HELIX:
+            ret = "Helix Propensity";
+
+            break;
+
+        case STRAND:
+            ret = "Strand Propensity";
+
+            break;
+
+        case TURN:
+            ret = "Turn Propensity";
+
+            break;
+
+        case BURIED:
+            ret = "Buried Index";
+
+            break;
+
+        case NUCLEOTIDE:
+            ret = "Nucleotide";
+
+            break;
+
+        case USER_DEFINED:
+            ret = "User Defined";
+
+            break;
+
+        default:
+            ret = "None";
+
+            break;
+        }
+
+        return ret;
+    }
+
+    /**
+     * 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);
+    }
+
+    /**
+     * 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)
+    {
+        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)
+    {
+        ColourSchemeI cs = null;
+
+        switch (index)
+        {
+        case CLUSTAL:
+            cs = new ClustalxColourScheme(seqs, width);
+
+            break;
+
+        case BLOSUM:
+            cs = new Blosum62ColourScheme();
+
+            break;
+
+        case PID:
+            cs = new PIDColourScheme();
+
+            break;
+
+        case ZAPPO:
+            cs = new ZappoColourScheme();
+
+            break;
+
+        case HYDROPHOBIC:
+            cs = new HydrophobicColourScheme();
+
+            break;
+
+        case HELIX:
+            cs = new HelixColourScheme();
+
+            break;
+
+        case STRAND:
+            cs = new StrandColourScheme();
+
+            break;
+
+        case TURN:
+            cs = new TurnColourScheme();
+
+            break;
+
+        case BURIED:
+            cs = new BuriedColourScheme();
+
+            break;
+
+        case NUCLEOTIDE:
+            cs = new NucleotideColourScheme();
+
+            break;
+
+        case USER_DEFINED:
+            cs = new UserColourScheme(new Color[0]);
+
+            break;
+
+        default:
+            break;
+        }
+
+        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;
+    }
 }