/*\r
- * Jalview - A Sequence Alignment Editor and Viewer\r
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
- *\r
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)\r
+ * Copyright (C) 2008 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
+ * \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
+ * \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
import jalview.schemes.*;\r
\r
/**\r
- * Parse and create Jalview Features files\r
- * Detects GFF format features files and parses.\r
- * Does not implement standard print() - call specific printFeatures or printGFF.\r
- * Uses AlignmentI.findSequence(String id) to find the sequence object for the features annotation - this normally works on an exact match.\r
+ * Parse and create Jalview Features files Detects GFF format features files and\r
+ * parses. Does not implement standard print() - call specific printFeatures or\r
+ * printGFF. Uses AlignmentI.findSequence(String id) to find the sequence object\r
+ * for the features annotation - this normally works on an exact match.\r
+ * \r
* @author AMW\r
* @version $Revision$\r
*/\r
-public class FeaturesFile\r
- extends AlignFile\r
+public class FeaturesFile extends AlignFile\r
{\r
/**\r
* Creates a new FeaturesFile object.\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
+ * @param inFile\r
+ * DOCUMENT ME!\r
+ * @param type\r
+ * DOCUMENT ME!\r
+ * \r
+ * @throws IOException\r
+ * DOCUMENT ME!\r
*/\r
- public FeaturesFile(String inFile, String type)\r
- throws IOException\r
+ public FeaturesFile(String inFile, String type) throws IOException\r
{\r
super(inFile, type);\r
}\r
+\r
public FeaturesFile(FileParse source) throws IOException\r
{\r
super(source);\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
+ * The Application can render HTML, but the applet will remove HTML tags and\r
+ * replace links with %LINK% Both need to read links in HTML however\r
+ * \r
+ * @throws IOException\r
+ * DOCUMENT ME!\r
*/\r
- public boolean parse(AlignmentI align,\r
- Hashtable colours,\r
- boolean removeHTML)\r
+ public boolean parse(AlignmentI align, 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
+ * The Application can render HTML, but the applet will remove HTML tags and\r
+ * replace links with %LINK% Both need to read links in HTML however\r
+ * \r
+ * @throws IOException\r
+ * DOCUMENT ME!\r
*/\r
- public boolean parse(AlignmentI align,\r
- Hashtable colours,\r
- Hashtable featureLink,\r
- boolean removeHTML)\r
+ public boolean parse(AlignmentI align, Hashtable colours,\r
+ Hashtable featureLink, boolean removeHTML)\r
{\r
String line = null;\r
try\r
\r
boolean GFFFile = true;\r
\r
- while ( (line = nextLine()) != null)\r
+ while ((line = nextLine()) != null)\r
{\r
if (line.startsWith("#"))\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
+ // 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
continue;\r
}\r
-\r
+ String seqId = "";\r
while (st.hasMoreElements())\r
{\r
\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, true);\r
+ seqId = token = st.nextToken();\r
+ seq = align.findName(seqId, true);\r
if (seq != null)\r
{\r
desc = st.nextToken();\r
type = st.nextToken();\r
- try {\r
- start = Integer.parseInt(st.nextToken());\r
+ try\r
+ {\r
+ start = Integer.parseInt(st.nextToken());\r
} catch (NumberFormatException ex)\r
{\r
- start=0;\r
+ start = 0;\r
}\r
- try {\r
+ try\r
+ {\r
end = Integer.parseInt(st.nextToken());\r
- }\r
- catch (NumberFormatException ex)\r
+ } catch (NumberFormatException ex)\r
{\r
- end=-1;\r
- } \r
+ end = -1;\r
+ }\r
try\r
{\r
score = new Float(st.nextToken()).floatValue();\r
- }\r
- catch (NumberFormatException ex)\r
+ } catch (NumberFormatException ex)\r
{\r
score = 0;\r
}\r
{\r
sf.setValue("STRAND", st.nextToken());\r
sf.setValue("FRAME", st.nextToken());\r
+ } catch (Exception ex)\r
+ {\r
}\r
- catch (Exception ex)\r
- {}\r
\r
if (st.hasMoreTokens())\r
{\r
}\r
\r
seq.addSequenceFeature(sf);\r
-\r
+ while ((seq = align.findName(seq, seqId, true)) != null)\r
+ {\r
+ seq.addSequenceFeature(new SequenceFeature(sf));\r
+ }\r
break;\r
}\r
}\r
}\r
if (!st.hasMoreTokens())\r
{\r
- System.err.println("DEBUG: Run out of tokens when trying to identify the destination for the feature.. giving up.");\r
- // in all probability, this isn't a file we understand, so bail quietly.\r
+ System.err\r
+ .println("DEBUG: Run out of tokens when trying to identify the destination for the feature.. giving up.");\r
+ // in all probability, this isn't a file we understand, so bail\r
+ // quietly.\r
return false;\r
}\r
- \r
+\r
token = st.nextToken();\r
- \r
+\r
if (!token.equals("ID_NOT_SPECIFIED"))\r
{\r
- seq = align.findName(token, true);\r
+ seq = align.findName(seqId = token, true);\r
st.nextToken();\r
}\r
else\r
{\r
+ seqId = null;\r
try\r
{\r
index = Integer.parseInt(st.nextToken());\r
seq = align.getSequenceAt(index);\r
- }\r
- catch (NumberFormatException ex)\r
+ } catch (NumberFormatException ex)\r
{\r
seq = null;\r
}\r
\r
sf = new SequenceFeature(type, desc, "", start, end, featureGroup);\r
\r
- seq.addSequenceFeature(sf);\r
-\r
if (groupLink != null && removeHTML)\r
{\r
sf.addLink(groupLink);\r
\r
parseDescriptionHTML(sf, removeHTML);\r
\r
- //If we got here, its not a GFFFile\r
+ seq.addSequenceFeature(sf);\r
+\r
+ while (seqId != null\r
+ && (seq = align.findName(seq, seqId, false)) != null)\r
+ {\r
+ seq.addSequenceFeature(new SequenceFeature(sf));\r
+ }\r
+ // If we got here, its not a GFFFile\r
GFFFile = false;\r
}\r
}\r
- }\r
- catch (Exception ex)\r
+ } catch (Exception ex)\r
{\r
System.out.println(line);\r
System.out.println("Error parsing feature file: " + ex + "\n" + line);\r
return;\r
}\r
\r
- if (removeHTML && sf.getDescription().toUpperCase().indexOf("<HTML>") == -1)\r
+ if (removeHTML\r
+ && sf.getDescription().toUpperCase().indexOf("<HTML>") == -1)\r
{\r
removeHTML = false;\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
+ * generate a features file for seqs\r
+ * \r
+ * @param seqs\r
+ * source of sequence features\r
+ * @param visible\r
+ * hash of feature types and colours\r
+ * @return features file contents\r
+ */\r
+ public String printJalviewFormat(SequenceI[] seqs, Hashtable visible)\r
+ {\r
+ return printJalviewFormat(seqs, visible, true);\r
+ }\r
+\r
+ /**\r
+ * generate a features file for seqs with colours from visible (if any)\r
+ * \r
+ * @param seqs\r
+ * source of features\r
+ * @param visible\r
+ * hash of Colours for each feature type\r
+ * @param visOnly\r
+ * when true only feature types in 'visible' will be output\r
+ * @return features file contents\r
*/\r
- public String printJalviewFormat(SequenceI[] seqs,\r
- Hashtable visible)\r
+ public String printJalviewFormat(SequenceI[] seqs, Hashtable visible,\r
+ boolean visOnly)\r
{\r
StringBuffer out = new StringBuffer();\r
SequenceFeature[] next;\r
\r
- if (visible == null || visible.size() < 1)\r
+ if (visOnly && (visible == null || visible.size() < 1))\r
{\r
return "No Features Visible";\r
}\r
-\r
- Enumeration en = visible.keys();\r
- String type;\r
- int color;\r
- while (en.hasMoreElements())\r
+ if (visible != null && visOnly)\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
+ // write feature colours only if we're given them and we are generating\r
+ // viewed features\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\r
+ + "\t"\r
+ + jalview.util.Format\r
+ .getHexString(new java.awt.Color(color)) + "\n");\r
+ }\r
}\r
-\r
- //Work out which groups are both present and visible\r
+ // Work out which groups are both present and visible\r
Vector groups = new Vector();\r
int groupIndex = 0;\r
\r
{\r
for (int j = 0; j < next.length; j++)\r
{\r
- if (!visible.containsKey(next[j].type))\r
+ if (visOnly && !visible.containsKey(next[j].type))\r
{\r
continue;\r
}\r
\r
if (next[j].featureGroup != null\r
- && !groups.contains(next[j].featureGroup))\r
+ && !groups.contains(next[j].featureGroup))\r
{\r
groups.addElement(next[j].featureGroup);\r
}\r
{\r
for (int j = 0; j < next.length; j++)\r
{\r
- if (!visible.containsKey(next[j].type))\r
+ if (visOnly && !visible.containsKey(next[j].type))\r
{\r
continue;\r
}\r
\r
if (group != null\r
- && (next[j].featureGroup == null\r
- || !next[j].featureGroup.equals(group))\r
- )\r
+ && (next[j].featureGroup == null || !next[j].featureGroup\r
+ .equals(group)))\r
{\r
continue;\r
}\r
continue;\r
}\r
\r
- if (next[j].description == null || next[j].description.equals(""))\r
+ if (next[j].description == null\r
+ || 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
+ && next[j].getDescription().indexOf("<html>") == -1)\r
{\r
out.append("<html>");\r
}\r
\r
if (next[j].description.indexOf(href) == -1)\r
{\r
- out.append("<a href=\""\r
- + href\r
- + "\">"\r
- + label\r
- + "</a>");\r
+ out\r
+ .append("<a href=\"" + href + "\">" + label\r
+ + "</a>");\r
}\r
}\r
\r
out.append("\t");\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
+ out.append(seqs[i].getName() + "\t-1\t" + next[j].begin + "\t"\r
+ + next[j].end + "\t" + next[j].type + "\n");\r
}\r
}\r
}\r
break;\r
}\r
\r
- }\r
- while (groupIndex < groups.size() + 1);\r
+ } while (groupIndex < groups.size() + 1);\r
\r
return out.toString();\r
}\r
\r
public String printGFFFormat(SequenceI[] seqs, Hashtable visible)\r
{\r
+ return printGFFFormat(seqs, visible, true);\r
+ }\r
+\r
+ public String printGFFFormat(SequenceI[] seqs, Hashtable visible,\r
+ boolean visOnly)\r
+ {\r
StringBuffer out = new StringBuffer();\r
SequenceFeature[] next;\r
String source;\r
next = seqs[i].getSequenceFeatures();\r
for (int j = 0; j < next.length; j++)\r
{\r
- if (!visible.containsKey(next[j].type))\r
+ if (visOnly && !visible.containsKey(next[j].type))\r
{\r
continue;\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" + source + "\t"\r
+ + next[j].type + "\t" + next[j].begin + "\t"\r
+ + next[j].end + "\t" + next[j].score + "\t");\r
\r
if (next[j].getValue("STRAND") != null)\r
{\r
return out.toString();\r
}\r
\r
+ /**\r
+ * this is only for the benefit of object polymorphism - method does nothing.\r
+ */\r
public void parse()\r
{\r
- //IGNORED\r
+ // IGNORED\r
}\r
\r
/**\r
- * DOCUMENT ME!\r
- *\r
- * @return DOCUMENT ME!\r
+ * this is only for the benefit of object polymorphism - method does nothing.\r
+ * \r
+ * @return error message\r
*/\r
public String print()\r
{\r
git://source.jalview.org / jalview.git / blobdiff