X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fext%2Fso%2FSequenceOntology.java;h=5a86fa10ec4cbd24a010e5ac6c5c53e9760cfe06;hb=a62e172dc725a573a85ca49552020cc75cfdc1f1;hp=af80b7a0efbe2ae52d4c0c3ca269bd44d22fed30;hpb=d3d566fbf876a3511c06fecec695b2f59eb71169;p=jalview.git
diff --git a/src/jalview/ext/so/SequenceOntology.java b/src/jalview/ext/so/SequenceOntology.java
index af80b7a..5a86fa1 100644
--- a/src/jalview/ext/so/SequenceOntology.java
+++ b/src/jalview/ext/so/SequenceOntology.java
@@ -1,3 +1,23 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
package jalview.ext.so;
import jalview.io.gff.SequenceOntologyI;
@@ -62,10 +82,10 @@ public class SequenceOntology implements SequenceOntologyI
*/
public SequenceOntology()
{
- termsFound = new ArrayList();
- termsNotFound = new ArrayList();
- termsByDescription = new HashMap();
- termIsA = new HashMap>();
+ termsFound = new ArrayList<>();
+ termsNotFound = new ArrayList<>();
+ termsByDescription = new HashMap<>();
+ termIsA = new HashMap<>();
loadOntologyZipFile("so-xp-simple.obo");
}
@@ -77,13 +97,13 @@ public class SequenceOntology implements SequenceOntologyI
*/
protected void loadOntologyZipFile(String ontologyFile)
{
+ long now = System.currentTimeMillis();
ZipInputStream zipStream = null;
try
{
String zipFile = ontologyFile + ".zip";
- System.out.println("Loading Sequence Ontology from " + zipFile);
- InputStream inStream = this.getClass().getResourceAsStream(
- "/" + zipFile);
+ InputStream inStream = this.getClass()
+ .getResourceAsStream("/" + zipFile);
zipStream = new ZipInputStream(new BufferedInputStream(inStream));
ZipEntry entry;
while ((entry = zipStream.getNextEntry()) != null)
@@ -93,6 +113,9 @@ public class SequenceOntology implements SequenceOntologyI
loadOboFile(zipStream);
}
}
+ long elapsed = System.currentTimeMillis() - now;
+ System.out.println("Loaded Sequence Ontology from " + zipFile + " ("
+ + elapsed + "ms)");
} catch (Exception e)
{
e.printStackTrace();
@@ -128,8 +151,8 @@ public class SequenceOntology implements SequenceOntologyI
* @throws ParseException
* @throws IOException
*/
- protected void loadOboFile(InputStream is) throws ParseException,
- IOException
+ protected void loadOboFile(InputStream is)
+ throws ParseException, IOException
{
BufferedReader oboFile = new BufferedReader(new InputStreamReader(is));
OboParser parser = new OboParser();
@@ -172,9 +195,9 @@ public class SequenceOntology implements SequenceOntologyI
}
else
{
- System.err.println("Warning: " + term.getName()
- + " has replaced " + replaced.getName()
- + " for lookup of '" + description + "'");
+ System.err.println("Warning: " + term.getName()
+ + " has replaced " + replaced.getName()
+ + " for lookup of '" + description + "'");
}
}
termsByDescription.put(description, term);
@@ -197,8 +220,8 @@ public class SequenceOntology implements SequenceOntologyI
{
try
{
- if (Boolean.TRUE.equals(ann.getProperty("is_obsolete")))
- {
+ if (Boolean.TRUE.equals(ann.getProperty("is_obsolete")))
+ {
return true;
}
} catch (NoSuchElementException e)
@@ -381,7 +404,7 @@ public class SequenceOntology implements SequenceOntologyI
*/
protected synchronized void findParents(Term childTerm)
{
- List result = new ArrayList();
+ List result = new ArrayList<>();
for (Triple triple : ontology.getTriples(childTerm, null, isA))
{
Term parent = triple.getObject();