"JALVIEW_ANNOTATION\n"\r
+ "# Created: "\r
+ new java.util.Date() + "\n\n");\r
-\r
+ /**\r
+ * convenience method for pre-2.4 feature files which have no view, hidden columns or hidden row keywords.\r
+ * @param annotations\r
+ * @param groups\r
+ * @param properties\r
+ * @return feature file as a string.\r
+ */\r
public String printAnnotations(AlignmentAnnotation[] annotations,\r
Vector groups,\r
Hashtable properties)\r
{\r
+ return printAnnotations(annotations, groups,\r
+ properties, null);\r
+\r
+ }\r
+ /**\r
+ * hold all the information about a particular view definition\r
+ * read from or written out in an annotations file.\r
+ */\r
+ public class ViewDef {\r
+ public String viewname;\r
+ public HiddenSequences hidseqs;\r
+ public ColumnSelection hiddencols;\r
+ public Vector visibleGroups;\r
+ public ViewDef(String viewname, HiddenSequences hidseqs,\r
+ ColumnSelection hiddencols)\r
+ {\r
+ this.viewname = viewname;\r
+ this.hidseqs = hidseqs;\r
+ this.hiddencols = hiddencols;\r
+ }\r
+ }\r
+ public String printAnnotations(AlignmentAnnotation[] annotations,\r
+ Vector groups,\r
+ Hashtable properties, ViewDef[] views)\r
+ {\r
if (annotations != null)\r
{\r
+ boolean oneColour = true;\r
AlignmentAnnotation row;\r
String comma;\r
SequenceI refSeq = null;\r
{\r
row = annotations[i];\r
\r
- if (!row.visible)\r
+ if (!row.visible && !row.hasScore())\r
{\r
continue;\r
}\r
\r
color = null;\r
+ oneColour = true;\r
\r
if (row.sequenceRef == null)\r
{\r
text.append(row.description + "\t");\r
}\r
\r
- for (int j = 0; j < row.annotations.length; j++)\r
+ for (int j = 0; row.annotations!=null && j < row.annotations.length; j++)\r
{\r
if (refSeq != null &&\r
jalview.util.Comparison.isGap(refSeq.getCharAt(j)))\r
\r
if (row.annotations[j] != null)\r
{\r
+ if(color!=null && !color.equals(row.annotations[j].colour))\r
+ {\r
+ oneColour = false;\r
+ }\r
+\r
color = row.annotations[j].colour;\r
if (row.annotations[j].value != 0f)\r
{\r
\r
text.append("\n");\r
\r
- if (color != null && color != java.awt.Color.black)\r
+ if (color != null && color != java.awt.Color.black && oneColour)\r
{\r
colours.append("COLOUR\t"\r
+ row.label + "\t"\r
}\r
\r
}\r
-\r
+ \r
return text.toString();\r
}\r
\r
\r
annotation = new AlignmentAnnotation(label,\r
description,\r
- annotations,\r
+ (index==0) ? null : annotations,\r
0,\r
0,\r
graphStyle);\r
\r
}\r
\r
- if (displayChar.length() > 1\r
+ if (displayChar!=null\r
+ && displayChar.length() > 1\r
&& desc!=null\r
&& desc.length() == 1)\r
{\r
displayChar = desc;\r
desc = tmp;\r
}\r
-\r
+ /*\r
+ * In principle, this code will ensure that the Annotation element generated is renderable by any of the applet or application rendering code\r
+ * but instead we check for null strings when the display character is rendered. \r
+ if (displayChar==null)\r
+ {\r
+ displayChar="";\r
+ }\r
+ */\r
Annotation anot = new Annotation(displayChar, desc, ss, value);\r
\r
anot.colour = colour;\r
al.setProperty(key,value);\r
}\r
}\r
+\r
+ /**\r
+ * Write annotations as a CSV file of the form 'label, value, value, ...' for each row.\r
+ * @param annotations\r
+ * @return CSV file as a string.\r
+ */\r
+ public String printCSVAnnotations(AlignmentAnnotation[] annotations)\r
+ {\r
+ StringBuffer sp = new StringBuffer();\r
+ for (int i=0; i<annotations.length; i++)\r
+ {\r
+ String atos = annotations[i].toString();\r
+ int p = 0;\r
+ do {\r
+ int cp = atos.indexOf("\n", p);\r
+ sp.append(annotations[i].label);\r
+ sp.append(",");\r
+ if (cp>p)\r
+ {\r
+ sp.append(atos.substring(p, cp+1));\r
+ } else {\r
+ sp.append(atos.substring(p));\r
+ sp.append("\n");\r
+ }\r
+ p = cp+1;\r
+ } while (p>0);\r
+ }\r
+ return sp.toString();\r
+ }\r
}\r