From 9967bbf3d9c8e015662f09f5ec1b363333f0b117 Mon Sep 17 00:00:00 2001 From: Jim Procter Date: Mon, 17 Nov 2014 14:42:21 +0000 Subject: [PATCH] imports and formatting --- src/jalview/ws/jws1/JPredThread.java | 33 +++++++++++++++++++++------------ 1 file changed, 21 insertions(+), 12 deletions(-) diff --git a/src/jalview/ws/jws1/JPredThread.java b/src/jalview/ws/jws1/JPredThread.java index dc245ae..72274de 100644 --- a/src/jalview/ws/jws1/JPredThread.java +++ b/src/jalview/ws/jws1/JPredThread.java @@ -20,17 +20,26 @@ */ package jalview.ws.jws1; -import java.util.*; - -import jalview.analysis.*; -import jalview.bin.*; -import jalview.datamodel.*; -import jalview.gui.*; -import jalview.io.*; -import jalview.util.*; +import jalview.analysis.AlignSeq; +import jalview.bin.Cache; +import jalview.datamodel.Alignment; +import jalview.datamodel.AlignmentAnnotation; +import jalview.datamodel.AlignmentView; +import jalview.datamodel.ColumnSelection; +import jalview.datamodel.SequenceI; +import jalview.gui.AlignFrame; +import jalview.gui.Desktop; +import jalview.gui.WebserviceInfo; +import jalview.io.FormatAdapter; +import jalview.util.Comparison; +import jalview.util.MessageManager; import jalview.ws.AWsJob; import jalview.ws.JobStateSummary; import jalview.ws.WSClientI; + +import java.util.Hashtable; +import java.util.List; + import vamsas.objects.simple.JpredResult; class JPredThread extends JWS1Thread implements WSClientI @@ -138,7 +147,7 @@ class JPredThread extends JWS1Thread implements WSClientI sqs[i] = al.getSequenceAt(i); } if (!jalview.analysis.SeqsetUtils.deuniquify( - (Hashtable) SequenceInfo, sqs)) + SequenceInfo, sqs)) { throw (new Exception(MessageManager.getString("exception.couldnt_recover_sequence_properties_for_alignment"))); } @@ -169,8 +178,8 @@ class JPredThread extends JWS1Thread implements WSClientI if (predMap != null) { char gc = getGapChar(); - SequenceI[] sqs = (SequenceI[]) ((java.lang.Object[]) input - .getAlignmentAndColumnSelection(gc))[0]; + SequenceI[] sqs = (SequenceI[]) input + .getAlignmentAndColumnSelection(gc)[0]; if (this.msaIndex >= sqs.length) { throw new Error(MessageManager.getString("error.implementation_error_invalid_msa_index_for_job")); @@ -428,7 +437,7 @@ class JPredThread extends JWS1Thread implements WSClientI { if (job.getJobId().startsWith("Broken")) { - job.result = (vamsas.objects.simple.Result) new JpredResult(); + job.result = new JpredResult(); job.result.setInvalid(true); job.result.setStatus(MessageManager.formatMessage("label.submission_params", new String[]{job.getJobId().toString()})); throw new Exception(job.getJobId()); -- 1.7.10.2