X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fio%2Fpacked%2FParsePackedSet.java;h=91575bfd7403b6674a1f7b5ac65e7673d0cb613d;hb=ae91bd2b6c74d4b6267d0df5670db7207707130b;hp=20b2061e33b80fa565f2d4537c76969e3c5180cf;hpb=2ddb613232cf825e989a5b0e7772f83a09dd682e;p=jalview.git
diff --git a/src/jalview/io/packed/ParsePackedSet.java b/src/jalview/io/packed/ParsePackedSet.java
index 20b2061..91575bf 100644
--- a/src/jalview/io/packed/ParsePackedSet.java
+++ b/src/jalview/io/packed/ParsePackedSet.java
@@ -1,16 +1,40 @@
+/*
+ * 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;
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;
+import java.util.Locale;
public class ParsePackedSet
{
@@ -42,10 +66,10 @@ 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;
@@ -54,31 +78,24 @@ 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);
- 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;
}
}
}
@@ -101,8 +118,16 @@ public class ParsePackedSet
{
br = new BufferedReader(src.getReader());
}
- 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
+ {
+ errmsg = "Annotation file contained no data.";
+ }
} catch (Exception e)
{
@@ -123,16 +148,18 @@ public class ParsePackedSet
}
if (dta.getType().equals(JvDataType.FEATURES))
{
- // check the context has a place to store feature rendering definitions, if not, create one.
- if (context.featureColours==null)
+ // check the context has a place to store feature rendering definitions,
+ // 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);
- ff.parse(context.getLastAlignment(), context.featureColours,
- false);
+ context.updateSetModified(ff.parse(context.getLastAlignment(),
+ context.featureColours, false,
+ context.relaxedIdMatching));
} catch (Exception e)
{
errmsg = ("Failed to parse the Features file associated with the alignment.");
@@ -155,6 +182,7 @@ public class ParsePackedSet
context.addTreeFromFile(nf);
rslt.add(nf);
+ context.updateSetModified(true);
}
} catch (Exception e)
{
@@ -163,7 +191,24 @@ public class ParsePackedSet
}
}
-
+ if (exerror != null)
+ {
+ if (errmsg != null && errmsg.length() > 0)
+ {
+ throw new IOException(errmsg, exerror);
+ }
+ else
+ {
+ throw new IOException(errmsg, exerror);
+ }
+ }
+ else
+ {
+ if (errmsg != null && errmsg.length() > 0)
+ {
+ throw new IOException(errmsg);
+ }
+ }
}
if (deuniquify)
{
@@ -189,8 +234,8 @@ public class ParsePackedSet
{
String type = args[i++];
final String file = args[i++];
- final JvDataType jtype = DataProvider.JvDataType.valueOf(type
- .toUpperCase());
+ final JvDataType jtype = DataProvider.JvDataType
+ .valueOf(type.toUpperCase(Locale.ROOT));
if (jtype != null)
{
final FileParse fp;
@@ -209,7 +254,7 @@ public class ParsePackedSet
else
{
System.out.println("Couldn't parse source type token '"
- + type.toUpperCase() + "'");
+ + type.toUpperCase(Locale.ROOT) + "'");
}
}
if (i < args.length)
@@ -228,8 +273,8 @@ public class ParsePackedSet
ParsePackedSet pps;
try
{
- newdm = (pps = new ParsePackedSet()).getAlignment(
- context = new JalviewDataset(), dp);
+ newdm = (pps = new ParsePackedSet())
+ .getAlignment(context = new JalviewDataset(), dp);
} catch (Exception e)
{
System.out.println("Test failed for these arguments.\n");
@@ -249,5 +294,13 @@ public class ParsePackedSet
// import with deuniquify info, and compare results to input.
}
+ else
+ {
+ if (context.getLastAlignmentSet().isModified())
+ {
+ System.err.println(
+ "Initial alignment set was modified and any associated views should be updated.");
+ }
+ }
}
}