X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2Fpacked%2FParsePackedSet.java;h=138fef717606bb6e7af189c2390a9f5457212daf;hb=ff8c06845590fd9fd423aa59809dcce9610ab295;hp=9a4af6294bbcb0f2360eebb23f15d152ec1993cd;hpb=c666f8aee30822a9d8e8932041707587b5cffb70;p=jalview.git
diff --git a/src/jalview/io/packed/ParsePackedSet.java b/src/jalview/io/packed/ParsePackedSet.java
index 9a4af62..138fef7 100644
--- a/src/jalview/io/packed/ParsePackedSet.java
+++ b/src/jalview/io/packed/ParsePackedSet.java
@@ -1,7 +1,29 @@
+/*
+ * 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.io.packed;
+import jalview.api.FeatureColourI;
import jalview.datamodel.AlignmentI;
import jalview.io.AppletFormatAdapter;
+import jalview.io.FileFormatI;
import jalview.io.FileParse;
import jalview.io.FormatAdapter;
import jalview.io.IdentifyFile;
@@ -10,7 +32,7 @@ import jalview.io.packed.DataProvider.JvDataType;
import java.io.BufferedReader;
import java.io.IOException;
import java.util.ArrayList;
-import java.util.Hashtable;
+import java.util.HashMap;
import java.util.List;
public class ParsePackedSet
@@ -43,10 +65,10 @@ public class ParsePackedSet
FileParse src = dta.getDataSource();
if (dta.getType().equals(DataProvider.JvDataType.ALIGNMENT))
{
- String fmt = null;
+ FileFormatI fmt = null;
try
{
- fmt = new IdentifyFile().Identify(src, false);
+ fmt = new IdentifyFile().identify(src, false);
} catch (Exception ex)
{
exerror = ex;
@@ -55,32 +77,24 @@ public class ParsePackedSet
if (fmt != null)
{
- if (!FormatAdapter.isValidIOFormat(fmt, false))
+ // parse the alignment
+ AlignmentI al = null;
+ try
{
- errmsg = fmt;
- exerror = null;
+ al = new FormatAdapter().readFromFile(src, fmt);
+ } catch (Exception e)
+ {
+ errmsg = "Failed to parse alignment from result set";
+ exerror = e;
}
- else
+ if (al != null)
{
- // parse the alignment
- AlignmentI al = null;
- try
- {
- al = new FormatAdapter().readFromFile(src, fmt);
- } catch (Exception e)
- {
- errmsg = "Failed to parse alignment from result set";
- exerror = e;
- }
- if (al != null)
- {
- // deuniquify and construct/merge additional dataset entries if
- // necessary.
- context.addAlignment(al);
- context.updateSetModified(true);
- rslt.add(al);
- deuniquify = true;
- }
+ // deuniquify and construct/merge additional dataset entries if
+ // necessary.
+ context.addAlignment(al);
+ context.updateSetModified(true);
+ rslt.add(al);
+ deuniquify = true;
}
}
}
@@ -103,11 +117,14 @@ public class ParsePackedSet
{
br = new BufferedReader(src.getReader());
}
- if (new jalview.io.AnnotationFile()
- .parseAnnotationFrom(context.getLastAlignment(), br))
+ // TODO: add columnSelection to context
+ if (new jalview.io.AnnotationFile().parseAnnotationFrom(
+ context.getLastAlignment(), null, br))
{
context.updateSetModified(true);
- } else {
+ }
+ else
+ {
errmsg = "Annotation file contained no data.";
}
@@ -134,12 +151,12 @@ public class ParsePackedSet
// if not, create one.
if (context.featureColours == null)
{
- context.featureColours = new Hashtable();
+ context.featureColours = new HashMap();
}
try
{
jalview.io.FeaturesFile ff = new jalview.io.FeaturesFile(src);
- context.updateSetModified(ff.parse(context.getLastAlignment(),
+ context.updateSetModified(ff.parse(context.getLastAlignment(),
context.featureColours, false, context.relaxedIdMatching));
} catch (Exception e)
{
@@ -172,19 +189,23 @@ public class ParsePackedSet
}
}
- if (exerror!=null)
+ if (exerror != null)
{
- if (errmsg!=null && errmsg.length()>0)
+ if (errmsg != null && errmsg.length() > 0)
{
- throw new IOException(errmsg,exerror);
- } else {
- throw new IOException(errmsg,exerror);
+ throw new IOException(errmsg, exerror);
+ }
+ else
+ {
+ throw new IOException(errmsg, exerror);
}
- } else {
- if (errmsg!=null && errmsg.length()>0)
- {
- throw new IOException(errmsg);
}
+ else
+ {
+ if (errmsg != null && errmsg.length() > 0)
+ {
+ throw new IOException(errmsg);
+ }
}
}
if (deuniquify)
@@ -270,10 +291,13 @@ public class ParsePackedSet
// to buffers.
// import with deuniquify info, and compare results to input.
- } else {
+ }
+ else
+ {
if (context.getLastAlignmentSet().isModified())
{
- System.err.println("Initial alignment set was modified and any associated views should be updated.");
+ System.err
+ .println("Initial alignment set was modified and any associated views should be updated.");
}
}
}