-/**
- *
- */
-package uk.ac.vamsas.test.objects;
-
-import org.apache.commons.logging.Log;
-import org.apache.commons.logging.LogFactory;
-
-import uk.ac.vamsas.objects.core.*;
-import uk.ac.vamsas.objects.utils.*;
-import uk.ac.vamsas.objects.utils.document.*;
-import uk.ac.vamsas.test.simpleclient.ArchiveReports;
-
-/**
- * @author jim
- * test XSD-Java binding classes in uk.ac.vamsas.objects.core
- */
-public class Core {
- static Log log = LogFactory.getLog(Core.class);
-
- /**
- *
- * complete any automatically completable entries in the dataset
- * @param ds
- */
- public static String user = "uk.ac.vamsas.test.objects.Core";
-
- public static void complete(DataSet ds) {
- Sequence[] q = ds.getSequence();
- for (int i=0,j=q.length; i<j; i++) {
- q[i].setStart(i+1);
- q[i].setEnd(q[i].getSequence().length()+i+1);
- }
- }
-
- public static VAMSAS getDemoVamsas() {
- VAMSAS v=new VAMSAS();
- DataSet ds = new DataSet();
- ds.addSequence(Seq.newSequence("Dummy1","ASDFLEQ",SymbolDictionary.STANDARD_AA, 5, 11));
- ds.addSequence(Seq.newSequence("Dummy2","ASFLEQ",SymbolDictionary.STANDARD_AA, 5, 10));
- ds.addSequence(Seq.newSequence("Dummy3","ADFEQ",SymbolDictionary.STANDARD_AA, 3, 7));
- ds.setProvenance(ProvenanceStuff.newProvenance(user, "constructed some dummy sequences"));
- complete(ds);
- v.addDataSet(ds);
- Alignment al = new Alignment();
- al.setProvenance(ProvenanceStuff.newProvenance(user, "Created dummy alignment"));
- // rely on newAlignmentSequence to set start/end correctly
- al.addAlignmentSequence(Seq.newAlignmentSequence("Aligned1", "ASDFLEQ", ds.getSequence(0), -1, -1));
- al.addAlignmentSequence(Seq.newAlignmentSequence("Aligned2", "AS-FLEQ", ds.getSequence(1), -1, -1));
- al.addAlignmentSequence(Seq.newAlignmentSequence("Aligned3", "A-DF-EQ", ds.getSequence(2), -1, -1));
- al.setGapChar("-");
- ds.addAlignment(al);
- // TODO: create annotations
- // TODO: create tree
- return v;
- }
- /**
- * @param args
- */
- public static void main(String[] args) {
-
- /**
- * test constants and controlled vocab utils
- */
- System.out.println("VersionEntries.compare(invalid, ALPHA) returned "+VersionEntries.compare("invalid", VersionEntries.ALPHA_VERSION));
- System.out.println("VersionEntries.compare(ALPHA, invalid) returned "+VersionEntries.compare(VersionEntries.ALPHA_VERSION, "invalid"));
- System.out.println("VersionEntries.compare(BETA, ALPHA) returned "+VersionEntries.compare(VersionEntries.BETA_VERSION,VersionEntries.ALPHA_VERSION));
- System.out.println("VersionEntries.compare(ALPHA, BETA) returned "+VersionEntries.compare(VersionEntries.ALPHA_VERSION,VersionEntries.BETA_VERSION));
- System.out.println("VersionEntries.compare(ALPHA, ALPHA) returned "+VersionEntries.compare(VersionEntries.ALPHA_VERSION,VersionEntries.ALPHA_VERSION));
- System.out.println("VersionEntries.compare(invalid, invalid) returned "+VersionEntries.compare("invalid", "invalid"));
- System.out.println("VersionEntries.latestVersion()="+VersionEntries.latestVersion()+
- ", dict_aa="+SymbolDictionary.STANDARD_AA+", dict_na="+SymbolDictionary.STANDARD_NA);
- /**
- * Test utils and autogenerated Vobject interfaces
- */
-
- VamsasDocument doc = DocumentStuff.newVamsasDocument(new VAMSAS[] { getDemoVamsas() },
- ProvenanceStuff.newProvenance("org.vamsas.objects.test.Core", "Created demo vamsasDocument"),
- VersionEntries.latestVersion());
- ArchiveReports.reportDocument(doc, null, true, System.out);
- }
-}
+/*\r
+ * This file is part of the Vamsas Client version 0.1. \r
+ * Copyright 2009 by Jim Procter, Iain Milne, Pierre Marguerite, \r
+ * Andrew Waterhouse and Dominik Lindner.\r
+ * \r
+ * Earlier versions have also been incorporated into Jalview version 2.4 \r
+ * since 2008, and TOPALi version 2 since 2007.\r
+ * \r
+ * The Vamsas Client is free software: you can redistribute it and/or modify\r
+ * it under the terms of the GNU Lesser General Public License as published by\r
+ * the Free Software Foundation, either version 3 of the License, or\r
+ * (at your option) any later version.\r
+ * \r
+ * The Vamsas Client 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 Lesser General Public License for more details.\r
+ * \r
+ * You should have received a copy of the GNU Lesser General Public License\r
+ * along with the Vamsas Client. If not, see <http://www.gnu.org/licenses/>.\r
+ */\r
+package uk.ac.vamsas.test.objects;\r
+\r
+import org.apache.commons.logging.Log;\r
+import org.apache.commons.logging.LogFactory;\r
+\r
+import uk.ac.vamsas.objects.core.*;\r
+import uk.ac.vamsas.objects.utils.*;\r
+import uk.ac.vamsas.objects.utils.document.*;\r
+import uk.ac.vamsas.test.simpleclient.ArchiveReports;\r
+\r
+/**\r
+ * @author jim test XSD-Java binding classes in uk.ac.vamsas.objects.core\r
+ */\r
+public class Core {\r
+ static Log log = LogFactory.getLog(Core.class);\r
+\r
+ /**\r
+ * \r
+ * complete any automatically completable entries in the dataset\r
+ * \r
+ * @param ds\r
+ */\r
+ public static String user = "uk.ac.vamsas.test.objects.Core";\r
+\r
+ public static void complete(DataSet ds) {\r
+ Sequence[] q = ds.getSequence();\r
+ for (int i = 0, j = q.length; i < j; i++) {\r
+ q[i].setStart(i + 1);\r
+ q[i].setEnd(q[i].getSequence().length() + i + 1);\r
+ }\r
+ }\r
+\r
+ public static VAMSAS getDemoVamsas() {\r
+ VAMSAS v = new VAMSAS();\r
+ DataSet ds = new DataSet();\r
+ ds.addSequence(Seq.newSequence("Dummy1", "ASDFLEQ",\r
+ SymbolDictionary.STANDARD_AA, 5, 11));\r
+ ds.addSequence(Seq.newSequence("Dummy2", "ASFLEQ",\r
+ SymbolDictionary.STANDARD_AA, 5, 10));\r
+ ds.addSequence(Seq.newSequence("Dummy3", "ADFEQ",\r
+ SymbolDictionary.STANDARD_AA, 3, 7));\r
+ ds.setProvenance(ProvenanceStuff.newProvenance(user,\r
+ "constructed some dummy sequences"));\r
+ complete(ds);\r
+ v.addDataSet(ds);\r
+ Alignment al = new Alignment();\r
+ al.setProvenance(ProvenanceStuff.newProvenance(user,\r
+ "Created dummy alignment"));\r
+ // rely on newAlignmentSequence to set start/end correctly\r
+ al.addAlignmentSequence(Seq.newAlignmentSequence("Aligned1", "ASDFLEQ", ds\r
+ .getSequence(0), -1, -1));\r
+ al.addAlignmentSequence(Seq.newAlignmentSequence("Aligned2", "AS-FLEQ", ds\r
+ .getSequence(1), -1, -1));\r
+ al.addAlignmentSequence(Seq.newAlignmentSequence("Aligned3", "A-DF-EQ", ds\r
+ .getSequence(2), -1, -1));\r
+ al.setGapChar("-");\r
+ ds.addAlignment(al);\r
+ // TODO: create annotations\r
+ // TODO: create tree\r
+ return v;\r
+ }\r
+\r
+ /**\r
+ * @param args\r
+ */\r
+ public static void main(String[] args) {\r
+\r
+ /**\r
+ * test constants and controlled vocab utils\r
+ */\r
+ System.out.println("VersionEntries.compare(invalid, ALPHA) returned "\r
+ + VersionEntries.compare("invalid", VersionEntries.ALPHA_VERSION));\r
+ System.out.println("VersionEntries.compare(ALPHA, invalid) returned "\r
+ + VersionEntries.compare(VersionEntries.ALPHA_VERSION, "invalid"));\r
+ System.out.println("VersionEntries.compare(BETA, ALPHA) returned "\r
+ + VersionEntries.compare(VersionEntries.BETA_VERSION,\r
+ VersionEntries.ALPHA_VERSION));\r
+ System.out.println("VersionEntries.compare(ALPHA, BETA) returned "\r
+ + VersionEntries.compare(VersionEntries.ALPHA_VERSION,\r
+ VersionEntries.BETA_VERSION));\r
+ System.out.println("VersionEntries.compare(ALPHA, ALPHA) returned "\r
+ + VersionEntries.compare(VersionEntries.ALPHA_VERSION,\r
+ VersionEntries.ALPHA_VERSION));\r
+ System.out.println("VersionEntries.compare(invalid, invalid) returned "\r
+ + VersionEntries.compare("invalid", "invalid"));\r
+ System.out.println("VersionEntries.latestVersion()="\r
+ + VersionEntries.latestVersion() + ", dict_aa="\r
+ + SymbolDictionary.STANDARD_AA + ", dict_na="\r
+ + SymbolDictionary.STANDARD_NA);\r
+ /**\r
+ * Test utils and autogenerated Vobject interfaces\r
+ */\r
+\r
+ VamsasDocument doc = DocumentStuff.newVamsasDocument(\r
+ new VAMSAS[] { getDemoVamsas() }, ProvenanceStuff.newProvenance(\r
+ "org.vamsas.objects.test.Core", "Created demo vamsasDocument"),\r
+ VersionEntries.latestVersion());\r
+ ArchiveReports.reportDocument(doc, null, true, System.out);\r
+ }\r
+}\r
git://source.jalview.org / vamsas.git / blobdiff