/*\r
-* Jalview - A Sequence Alignment Editor and Viewer\r
-* Copyright (C) 2006 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
+ * Jalview - A Sequence Alignment Editor and Viewer\r
+ * Copyright (C) 2007 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.io;\r
\r
-import jalview.datamodel.*;\r
-\r
import java.io.*;\r
import java.util.*;\r
-import jalview.schemes.UserColourScheme;\r
\r
+import jalview.datamodel.*;\r
+import jalview.schemes.*;\r
\r
/**\r
* DOCUMENT ME!\r
* @author $author$\r
* @version $Revision$\r
*/\r
-public class FeaturesFile extends AlignFile\r
+public class FeaturesFile\r
+ extends AlignFile\r
{\r
- /**\r
- * Creates a new FeaturesFile object.\r
- */\r
- public FeaturesFile()\r
- {\r
- }\r
+ /**\r
+ * Creates a new FeaturesFile object.\r
+ */\r
+ public FeaturesFile()\r
+ {\r
+ }\r
\r
+ /**\r
+ * Creates a new FeaturesFile object.\r
+ *\r
+ * @param inFile DOCUMENT ME!\r
+ * @param type DOCUMENT ME!\r
+ *\r
+ * @throws IOException DOCUMENT ME!\r
+ */\r
+ public FeaturesFile(String inFile, String type)\r
+ throws IOException\r
+ {\r
+ super(inFile, type);\r
+ }\r
\r
- /**\r
- * Creates a new FeaturesFile object.\r
- *\r
- * @param inFile DOCUMENT ME!\r
- * @param type DOCUMENT ME!\r
- *\r
- * @throws IOException DOCUMENT ME!\r
- */\r
- public FeaturesFile(String inFile, String type)\r
- throws IOException\r
- {\r
- super(inFile, type);\r
- }\r
+ /**\r
+ * The Application can render HTML, but the applet will\r
+ * remove HTML tags and replace links with %LINK%\r
+ * Both need to read links in HTML however\r
+ *\r
+ * @throws IOException DOCUMENT ME!\r
+ */\r
+ public boolean parse(AlignmentI align,\r
+ Hashtable colours,\r
+ boolean removeHTML)\r
+ {\r
+ return parse(align, colours, null, removeHTML);\r
+ }\r
\r
- /**\r
- * The Application can render HTML, but the applet will\r
- * remove HTML tags and replace links with %LINK%\r
- * Both need to read links in HTML however\r
- *\r
- * @throws IOException DOCUMENT ME!\r
- */\r
- public boolean parse(AlignmentI align,\r
- Hashtable colours,\r
- boolean removeHTML)\r
+ /**\r
+ * The Application can render HTML, but the applet will\r
+ * remove HTML tags and replace links with %LINK%\r
+ * Both need to read links in HTML however\r
+ *\r
+ * @throws IOException DOCUMENT ME!\r
+ */\r
+ public boolean parse(AlignmentI align,\r
+ Hashtable colours,\r
+ Hashtable featureLink,\r
+ boolean removeHTML)\r
+ {\r
+ String line = null;\r
+ try\r
{\r
- return parse(align, colours, null, removeHTML);\r
- }\r
- /**\r
- * The Application can render HTML, but the applet will\r
- * remove HTML tags and replace links with %LINK%\r
- * Both need to read links in HTML however\r
- *\r
- * @throws IOException DOCUMENT ME!\r
- */\r
- public boolean parse(AlignmentI align,\r
- Hashtable colours,\r
- Hashtable featureLink,\r
- boolean removeHTML)\r
- {\r
- String line = null;\r
- try\r
- {\r
- SequenceI seq = null;\r
- String type, desc, token=null;\r
+ SequenceI seq = null;\r
+ String type, desc, token = null;\r
\r
- int index, start, end;\r
- float score;\r
- StringTokenizer st;\r
- SequenceFeature sf;\r
- String featureGroup = null, groupLink = null;\r
- Hashtable typeLink = new Hashtable();\r
+ int index, start, end;\r
+ float score;\r
+ StringTokenizer st;\r
+ SequenceFeature sf;\r
+ String featureGroup = null, groupLink = null;\r
+ Hashtable typeLink = new Hashtable();\r
\r
- boolean GFFFile = true;\r
+ boolean GFFFile = true;\r
\r
- while ( (line = nextLine()) != null)\r
+ while ( (line = nextLine()) != null)\r
+ {\r
+ if (line.startsWith("#"))\r
{\r
- if(line.startsWith("#"))\r
- continue;\r
+ continue;\r
+ }\r
\r
- st = new StringTokenizer(line, "\t");\r
- if (st.countTokens()>1 && st.countTokens() < 4 )\r
+ st = new StringTokenizer(line, "\t");\r
+ if (st.countTokens() > 1 && st.countTokens() < 4)\r
+ {\r
+ GFFFile = false;\r
+ type = st.nextToken();\r
+ if (type.equalsIgnoreCase("startgroup"))\r
{\r
- GFFFile = false;\r
- type = st.nextToken();\r
- if (type.equalsIgnoreCase("startgroup"))\r
+ featureGroup = st.nextToken();\r
+ if (st.hasMoreElements())\r
{\r
- featureGroup = st.nextToken();\r
- if (st.hasMoreElements())\r
- {\r
- groupLink = st.nextToken();\r
- featureLink.put(featureGroup, groupLink);\r
- }\r
- }\r
- else if (type.equalsIgnoreCase("endgroup"))\r
- {\r
- //We should check whether this is the current group,\r
- //but at present theres no way of showing more than 1 group\r
- st.nextToken();\r
- featureGroup = null;\r
- groupLink = null;\r
+ groupLink = st.nextToken();\r
+ featureLink.put(featureGroup, groupLink);\r
}\r
- else\r
+ }\r
+ else if (type.equalsIgnoreCase("endgroup"))\r
+ {\r
+ //We should check whether this is the current group,\r
+ //but at present theres no way of showing more than 1 group\r
+ st.nextToken();\r
+ featureGroup = null;\r
+ groupLink = null;\r
+ }\r
+ else\r
+ {\r
+ UserColourScheme ucs = new UserColourScheme(st.nextToken());\r
+ colours.put(type, ucs.findColour('A'));\r
+ if (st.hasMoreElements())\r
{\r
- UserColourScheme ucs = new UserColourScheme(st.nextToken());\r
- colours.put(type, ucs.findColour('A'));\r
- if (st.hasMoreElements())\r
+ String link = st.nextToken();\r
+ typeLink.put(type, link);\r
+ if (featureLink == null)\r
{\r
- String link = st.nextToken();\r
- typeLink.put(type, link);\r
- if(featureLink==null)\r
- featureLink = new Hashtable();\r
- featureLink.put(type, link);\r
+ featureLink = new Hashtable();\r
}\r
-\r
+ featureLink.put(type, link);\r
}\r
- continue;\r
+\r
}\r
+ continue;\r
+ }\r
\r
- while (st.hasMoreElements())\r
- {\r
+ while (st.hasMoreElements())\r
+ {\r
\r
- if(GFFFile)\r
+ if (GFFFile)\r
+ {\r
+ // Still possible this is an old Jalview file,\r
+ // which does not have type colours at the beginning\r
+ token = st.nextToken();\r
+ seq = align.findName(token);\r
+ if (seq != null)\r
{\r
- // Still possible this is an old Jalview file,\r
- // which does not have type colours at the beginning\r
- token = st.nextToken();\r
- seq = align.findName(token);\r
- if(seq != null)\r
+ desc = st.nextToken();\r
+ type = st.nextToken();\r
+ start = Integer.parseInt(st.nextToken());\r
+ end = Integer.parseInt(st.nextToken());\r
+ try\r
{\r
- desc = st.nextToken();\r
- type = st.nextToken();\r
- start = Integer.parseInt(st.nextToken());\r
- end = Integer.parseInt(st.nextToken());\r
- try\r
- {\r
- score = new Float(st.nextToken()).floatValue();\r
- }\r
- catch (NumberFormatException ex)\r
- {\r
- score = 0;\r
- }\r
+ score = new Float(st.nextToken()).floatValue();\r
+ }\r
+ catch (NumberFormatException ex)\r
+ {\r
+ score = 0;\r
+ }\r
\r
- sf = new SequenceFeature(type, desc, start, end, score, null);\r
+ sf = new SequenceFeature(type, desc, start, end, score, null);\r
\r
- try\r
- {\r
- sf.setValue("STRAND", st.nextToken());\r
- sf.setValue("FRAME", st.nextToken());\r
- }\r
- catch (Exception ex)\r
- {}\r
+ try\r
+ {\r
+ sf.setValue("STRAND", st.nextToken());\r
+ sf.setValue("FRAME", st.nextToken());\r
+ }\r
+ catch (Exception ex)\r
+ {}\r
\r
- if(st.hasMoreTokens())\r
+ if (st.hasMoreTokens())\r
+ {\r
+ StringBuffer attributes = new StringBuffer();\r
+ while (st.hasMoreTokens())\r
{\r
- StringBuffer attributes = new StringBuffer();\r
- while (st.hasMoreTokens())\r
- {\r
- attributes.append("\t"+st.nextElement());\r
- }\r
- sf.setValue("ATTRIBUTES", attributes.toString());\r
+ attributes.append("\t" + st.nextElement());\r
}\r
-\r
- seq.addSequenceFeature(sf);\r
-\r
- break;\r
+ sf.setValue("ATTRIBUTES", attributes.toString());\r
}\r
- }\r
\r
- if(GFFFile && seq==null)\r
- {\r
- desc = token;\r
+ seq.addSequenceFeature(sf);\r
+\r
+ break;\r
}\r
- else\r
- desc = st.nextToken();\r
+ }\r
\r
+ if (GFFFile && seq == null)\r
+ {\r
+ desc = token;\r
+ }\r
+ else\r
+ {\r
+ desc = st.nextToken();\r
+ }\r
\r
- token = st.nextToken();\r
- if (!token.equals("ID_NOT_SPECIFIED"))\r
+ token = st.nextToken();\r
+ if (!token.equals("ID_NOT_SPECIFIED"))\r
+ {\r
+ seq = align.findName(token);\r
+ st.nextToken();\r
+ }\r
+ else\r
+ {\r
+ try\r
{\r
- seq = align.findName(token);\r
- st.nextToken();\r
+ index = Integer.parseInt(st.nextToken());\r
+ seq = align.getSequenceAt(index);\r
}\r
- else\r
+ catch (NumberFormatException ex)\r
{\r
- try{\r
- index = Integer.parseInt(st.nextToken());\r
- seq = align.getSequenceAt(index);\r
- }\r
- catch(NumberFormatException ex)\r
- {\r
- seq = null;\r
- }\r
+ seq = null;\r
}\r
+ }\r
\r
- if(seq==null)\r
- {\r
- System.out.println("Sequence not found: "+line);\r
- break;\r
- }\r
+ if (seq == null)\r
+ {\r
+ System.out.println("Sequence not found: " + line);\r
+ break;\r
+ }\r
\r
- start = Integer.parseInt(st.nextToken());\r
- end = Integer.parseInt(st.nextToken());\r
+ start = Integer.parseInt(st.nextToken());\r
+ end = Integer.parseInt(st.nextToken());\r
\r
- type = st.nextToken();\r
+ type = st.nextToken();\r
\r
- if (!colours.containsKey(type))\r
- {\r
- // Probably the old style groups file\r
- UserColourScheme ucs = new UserColourScheme(type);\r
- colours.put(type, ucs.findColour('A'));\r
- }\r
+ if (!colours.containsKey(type))\r
+ {\r
+ // Probably the old style groups file\r
+ UserColourScheme ucs = new UserColourScheme(type);\r
+ colours.put(type, ucs.findColour('A'));\r
+ }\r
\r
- sf = new SequenceFeature(type, desc, "", start, end, featureGroup);\r
+ sf = new SequenceFeature(type, desc, "", start, end, featureGroup);\r
\r
- seq.addSequenceFeature(sf);\r
+ seq.addSequenceFeature(sf);\r
\r
- if(groupLink!=null && removeHTML)\r
- {\r
- sf.addLink(groupLink);\r
- sf.description += "%LINK%";\r
- }\r
- if(typeLink.containsKey(type) && removeHTML)\r
- {\r
- sf.addLink(typeLink.get(type).toString());\r
- sf.description += "%LINK%";\r
- }\r
+ if (groupLink != null && removeHTML)\r
+ {\r
+ sf.addLink(groupLink);\r
+ sf.description += "%LINK%";\r
+ }\r
+ if (typeLink.containsKey(type) && removeHTML)\r
+ {\r
+ sf.addLink(typeLink.get(type).toString());\r
+ sf.description += "%LINK%";\r
+ }\r
\r
- parseDescriptionHTML(sf, removeHTML);\r
+ parseDescriptionHTML(sf, removeHTML);\r
\r
- //If we got here, its not a GFFFile\r
- GFFFile = false;\r
- }\r
+ //If we got here, its not a GFFFile\r
+ GFFFile = false;\r
}\r
}\r
- catch (Exception ex)\r
- {\r
- System.out.println(line);\r
- System.out.println("Error parsing feature file: " + ex +"\n"+line);\r
- return false;\r
- }\r
+ }\r
+ catch (Exception ex)\r
+ {\r
+ System.out.println(line);\r
+ System.out.println("Error parsing feature file: " + ex + "\n" + line);\r
+ return false;\r
+ }\r
+\r
+ return true;\r
+ }\r
+\r
+ public void parseDescriptionHTML(SequenceFeature sf, boolean removeHTML)\r
+ {\r
+ if (sf.getDescription() == null)\r
+ {\r
+ return;\r
+ }\r
\r
- return true;\r
+ if (removeHTML && sf.getDescription().toUpperCase().indexOf("<HTML>") == -1)\r
+ {\r
+ removeHTML = false;\r
}\r
\r
- public void parseDescriptionHTML(SequenceFeature sf, boolean removeHTML)\r
+ StringBuffer sb = new StringBuffer();\r
+ StringTokenizer st = new StringTokenizer(sf.getDescription(), "<");\r
+ String token, link;\r
+ int startTag;\r
+ String tag = null;\r
+ while (st.hasMoreElements())\r
{\r
- if(sf.getDescription()==null)\r
- return;\r
-\r
- if(removeHTML && sf.getDescription().toUpperCase().indexOf("<HTML>")==-1)\r
- removeHTML = false;\r
-\r
- StringBuffer sb = new StringBuffer();\r
- StringTokenizer st = new StringTokenizer(sf.getDescription(), "<");\r
- String token, link;\r
- int startTag;\r
- String tag=null;\r
- while(st.hasMoreElements())\r
+ token = st.nextToken("&>");\r
+ if (token.equalsIgnoreCase("html") || token.startsWith("/"))\r
{\r
- token = st.nextToken("&>");\r
- if(token.equalsIgnoreCase("html") || token.startsWith("/"))\r
- {\r
- continue;\r
- }\r
+ continue;\r
+ }\r
\r
- tag = null;\r
- startTag = token.indexOf("<");\r
+ tag = null;\r
+ startTag = token.indexOf("<");\r
\r
- if (startTag > -1)\r
- {\r
- tag = token.substring(startTag+1);\r
- token = token.substring(0, startTag);\r
- }\r
+ if (startTag > -1)\r
+ {\r
+ tag = token.substring(startTag + 1);\r
+ token = token.substring(0, startTag);\r
+ }\r
\r
- if (tag != null && tag.toUpperCase().startsWith("A HREF="))\r
- {\r
- if(token.length()>0)\r
- sb.append(token);\r
- link = tag.substring(tag.indexOf("\"") + 1, tag.length() - 1);\r
- String label = st.nextToken("<>");\r
- sf.addLink(label + "|" + link);\r
- sb.append(label + "%LINK%");\r
- }\r
- else if (tag != null && tag.equalsIgnoreCase("br"))\r
- sb.append("\n");\r
- else if (token.startsWith("lt;"))\r
- sb.append("<" + token.substring(3));\r
- else if (token.startsWith("gt;"))\r
- sb.append(">" + token.substring(3));\r
- else if (token.startsWith("amp;"))\r
- sb.append("&" + token.substring(4));\r
- else\r
+ if (tag != null && tag.toUpperCase().startsWith("A HREF="))\r
+ {\r
+ if (token.length() > 0)\r
{\r
sb.append(token);\r
}\r
+ link = tag.substring(tag.indexOf("\"") + 1, tag.length() - 1);\r
+ String label = st.nextToken("<>");\r
+ sf.addLink(label + "|" + link);\r
+ sb.append(label + "%LINK%");\r
+ }\r
+ else if (tag != null && tag.equalsIgnoreCase("br"))\r
+ {\r
+ sb.append("\n");\r
+ }\r
+ else if (token.startsWith("lt;"))\r
+ {\r
+ sb.append("<" + token.substring(3));\r
+ }\r
+ else if (token.startsWith("gt;"))\r
+ {\r
+ sb.append(">" + token.substring(3));\r
+ }\r
+ else if (token.startsWith("amp;"))\r
+ {\r
+ sb.append("&" + token.substring(4));\r
}\r
+ else\r
+ {\r
+ sb.append(token);\r
+ }\r
+ }\r
\r
- if(removeHTML)\r
- sf.description = sb.toString();\r
+ if (removeHTML)\r
+ {\r
+ sf.description = sb.toString();\r
+ }\r
\r
}\r
\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param s DOCUMENT ME!\r
- * @param len DOCUMENT ME!\r
- * @param gaps DOCUMENT ME!\r
- * @param displayId DOCUMENT ME!\r
- *\r
- * @return DOCUMENT ME!\r
- */\r
- public String printJalviewFormat(SequenceI [] seqs,\r
- Hashtable visible)\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param s DOCUMENT ME!\r
+ * @param len DOCUMENT ME!\r
+ * @param gaps DOCUMENT ME!\r
+ * @param displayId DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+ public String printJalviewFormat(SequenceI[] seqs,\r
+ Hashtable visible)\r
+ {\r
+ StringBuffer out = new StringBuffer();\r
+ SequenceFeature[] next;\r
+\r
+ if (visible == null || visible.size() < 1)\r
{\r
- StringBuffer out = new StringBuffer();\r
- SequenceFeature [] next;\r
-\r
- if(visible==null || visible.size()<1)\r
- return "No Features Visible";\r
+ return "No Features Visible";\r
+ }\r
\r
- Enumeration en = visible.keys();\r
- String type;\r
- int color;\r
- while( en.hasMoreElements() )\r
- {\r
- type = en.nextElement().toString();\r
- color = Integer.parseInt( visible.get(type).toString() );\r
- out.append(type + "\t"\r
- + jalview.util.Format.getHexString(\r
- new java.awt.Color(color) )\r
- +"\n");\r
- }\r
+ Enumeration en = visible.keys();\r
+ String type;\r
+ int color;\r
+ while (en.hasMoreElements())\r
+ {\r
+ type = en.nextElement().toString();\r
+ color = Integer.parseInt(visible.get(type).toString());\r
+ out.append(type + "\t"\r
+ + jalview.util.Format.getHexString(\r
+ new java.awt.Color(color))\r
+ + "\n");\r
+ }\r
\r
- //Work out which groups are both present and visible\r
- Vector groups = new Vector();\r
- int groupIndex = 0;\r
+ //Work out which groups are both present and visible\r
+ Vector groups = new Vector();\r
+ int groupIndex = 0;\r
\r
- for(int i=0; i<seqs.length; i++)\r
+ for (int i = 0; i < seqs.length; i++)\r
+ {\r
+ next = seqs[i].getSequenceFeatures();\r
+ if (next != null)\r
+ {\r
+ for (int j = 0; j < next.length; j++)\r
{\r
- next = seqs[i].getSequenceFeatures();\r
- if(next!=null)\r
+ if (!visible.containsKey(next[j].type))\r
{\r
- for(int j=0; j<next.length; j++)\r
- {\r
- if (!visible.containsKey(next[j].type))\r
- continue;\r
+ continue;\r
+ }\r
\r
- if ( next[j].featureGroup != null\r
- && !groups.contains(next[j].featureGroup))\r
- groups.addElement(next[j].featureGroup);\r
- }\r
+ if (next[j].featureGroup != null\r
+ && !groups.contains(next[j].featureGroup))\r
+ {\r
+ groups.addElement(next[j].featureGroup);\r
}\r
}\r
+ }\r
+ }\r
\r
- String group = null;\r
+ String group = null;\r
\r
- do\r
- {\r
+ do\r
+ {\r
\r
+ if (groups.size() > 0 && groupIndex < groups.size())\r
+ {\r
+ group = groups.elementAt(groupIndex).toString();\r
+ out.append("\nSTARTGROUP\t" + group + "\n");\r
+ }\r
+ else\r
+ {\r
+ group = null;\r
+ }\r
\r
- if (groups.size() > 0 && groupIndex < groups.size())\r
+ for (int i = 0; i < seqs.length; i++)\r
+ {\r
+ next = seqs[i].getSequenceFeatures();\r
+ if (next != null)\r
+ {\r
+ for (int j = 0; j < next.length; j++)\r
{\r
- group = groups.elementAt(groupIndex).toString();\r
- out.append("\nSTARTGROUP\t" + group + "\n");\r
- }\r
- else\r
- group = null;\r
+ if (!visible.containsKey(next[j].type))\r
+ {\r
+ continue;\r
+ }\r
\r
- for (int i = 0; i < seqs.length; i++)\r
- {\r
- next = seqs[i].getSequenceFeatures();\r
- if (next != null)\r
+ if (group != null\r
+ && (next[j].featureGroup == null\r
+ || !next[j].featureGroup.equals(group))\r
+ )\r
{\r
- for (int j = 0; j < next.length; j++)\r
- {\r
- if (!visible.containsKey(next[j].type))\r
- continue;\r
+ continue;\r
+ }\r
\r
- if (group != null\r
- && (next[j].featureGroup==null\r
- || !next[j].featureGroup.equals(group))\r
- )\r
- continue;\r
+ if (group == null && next[j].featureGroup != null)\r
+ {\r
+ continue;\r
+ }\r
\r
- if(group==null && next[j].featureGroup!=null)\r
- continue;\r
+ if (next[j].description == null || next[j].description.equals(""))\r
+ {\r
+ out.append(next[j].type + "\t");\r
+ }\r
+ else\r
+ {\r
+ if (next[j].links != null\r
+ && next[j].getDescription().indexOf("<html>") == -1)\r
+ {\r
+ out.append("<html>");\r
+ }\r
\r
- if(next[j].description==null || next[j].description.equals(""))\r
- out.append(next[j].type+"\t");\r
- else\r
+ out.append(next[j].description + " ");\r
+ if (next[j].links != null)\r
+ {\r
+ for (int l = 0; l < next[j].links.size(); l++)\r
{\r
- if(next[j].links!=null\r
- && next[j].getDescription().indexOf("<html>")==-1)\r
- out.append("<html>");\r
-\r
- out.append(next[j].description+" ");\r
- if(next[j].links!=null)\r
- {\r
- for(int l=0; l<next[j].links.size(); l++)\r
- {\r
- String label = next[j].links.elementAt(l).toString();\r
- String href = label.substring(label.indexOf("|")+1);\r
- label = label.substring(0, label.indexOf("|"));\r
-\r
- if(next[j].description.indexOf(href)==-1)\r
- {\r
- out.append("<a href=\""\r
- + href\r
- + "\">"\r
- + label\r
- + "</a>");\r
- }\r
- }\r
-\r
- if (next[j].getDescription().indexOf("</html>") == -1)\r
- out.append("</html>");\r
- }\r
-\r
-\r
- out.append("\t");\r
- }\r
+ String label = next[j].links.elementAt(l).toString();\r
+ String href = label.substring(label.indexOf("|") + 1);\r
+ label = label.substring(0, label.indexOf("|"));\r
\r
+ if (next[j].description.indexOf(href) == -1)\r
+ {\r
+ out.append("<a href=\""\r
+ + href\r
+ + "\">"\r
+ + label\r
+ + "</a>");\r
+ }\r
+ }\r
\r
- out.append( seqs[i].getName() + "\t-1\t"\r
- + next[j].begin + "\t"\r
- + next[j].end + "\t"\r
- + next[j].type + "\n"\r
- );\r
+ if (next[j].getDescription().indexOf("</html>") == -1)\r
+ {\r
+ out.append("</html>");\r
+ }\r
}\r
+\r
+ out.append("\t");\r
}\r
- }\r
\r
- if(group!=null)\r
- {\r
- out.append("ENDGROUP\t"+group+"\n");\r
- groupIndex++;\r
+ out.append(seqs[i].getName() + "\t-1\t"\r
+ + next[j].begin + "\t"\r
+ + next[j].end + "\t"\r
+ + next[j].type + "\n"\r
+ );\r
}\r
- else\r
- break;\r
-\r
}\r
- while(groupIndex < groups.size()+1);\r
+ }\r
\r
+ if (group != null)\r
+ {\r
+ out.append("ENDGROUP\t" + group + "\n");\r
+ groupIndex++;\r
+ }\r
+ else\r
+ {\r
+ break;\r
+ }\r
\r
- return out.toString();\r
}\r
+ while (groupIndex < groups.size() + 1);\r
\r
- public String printGFFFormat(SequenceI [] seqs, Hashtable visible)\r
- {\r
- StringBuffer out = new StringBuffer();\r
- SequenceFeature [] next;\r
- String source;\r
+ return out.toString();\r
+ }\r
+\r
+ public String printGFFFormat(SequenceI[] seqs, Hashtable visible)\r
+ {\r
+ StringBuffer out = new StringBuffer();\r
+ SequenceFeature[] next;\r
+ String source;\r
\r
- for(int i=0; i<seqs.length; i++)\r
+ for (int i = 0; i < seqs.length; i++)\r
+ {\r
+ if (seqs[i].getSequenceFeatures() != null)\r
{\r
- if(seqs[i].getSequenceFeatures()!=null)\r
+ next = seqs[i].getSequenceFeatures();\r
+ for (int j = 0; j < next.length; j++)\r
{\r
- next = seqs[i].getSequenceFeatures();\r
- for(int j=0; j<next.length; j++)\r
+ if (!visible.containsKey(next[j].type))\r
{\r
- if(!visible.containsKey(next[j].type))\r
- continue;\r
+ continue;\r
+ }\r
\r
- source = next[j].featureGroup;\r
- if(source==null)\r
- source = next[j].getDescription();\r
+ source = next[j].featureGroup;\r
+ if (source == null)\r
+ {\r
+ source = next[j].getDescription();\r
+ }\r
\r
- out.append(seqs[i].getName() + "\t"\r
- + source + "\t"\r
- + next[j].type + "\t"\r
- + next[j].begin + "\t"\r
- + next[j].end + "\t"\r
- + next[j].score + "\t"\r
- );\r
+ out.append(seqs[i].getName() + "\t"\r
+ + source + "\t"\r
+ + next[j].type + "\t"\r
+ + next[j].begin + "\t"\r
+ + next[j].end + "\t"\r
+ + next[j].score + "\t"\r
+ );\r
\r
- if(next[j].getValue("STRAND")!=null)\r
- out.append(next[j].getValue("STRAND")+"\t");\r
- else\r
- out.append(".\t");\r
+ if (next[j].getValue("STRAND") != null)\r
+ {\r
+ out.append(next[j].getValue("STRAND") + "\t");\r
+ }\r
+ else\r
+ {\r
+ out.append(".\t");\r
+ }\r
\r
- if(next[j].getValue("FRAME")!=null)\r
- out.append(next[j].getValue("FRAME"));\r
- else\r
- out.append(".");\r
+ if (next[j].getValue("FRAME") != null)\r
+ {\r
+ out.append(next[j].getValue("FRAME"));\r
+ }\r
+ else\r
+ {\r
+ out.append(".");\r
+ }\r
\r
- if(next[j].getValue("ATTRIBUTES")!=null)\r
- out.append(next[j].getValue("ATTRIBUTES"));\r
+ if (next[j].getValue("ATTRIBUTES") != null)\r
+ {\r
+ out.append(next[j].getValue("ATTRIBUTES"));\r
+ }\r
\r
- out.append("\n");\r
+ out.append("\n");\r
\r
- }\r
}\r
}\r
-\r
- return out.toString();\r
}\r
\r
- public void parse()\r
- {\r
- //IGNORED\r
- }\r
+ return out.toString();\r
+ }\r
\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @return DOCUMENT ME!\r
- */\r
- public String print()\r
- {\r
- return "USE printGFFFormat() or printJalviewFormat()";\r
- }\r
+ public void parse()\r
+ {\r
+ //IGNORED\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+ public String print()\r
+ {\r
+ return "USE printGFFFormat() or printJalviewFormat()";\r
+ }\r
}\r
git://source.jalview.org / jalview.git / blobdiff