X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2Fstructurechooser%2FStructureChooserQuerySource.java;h=cdf0d57405ae6d90aebdb55a09a850b1ad6af35a;hb=353cb52722490edcba2c13b18836b6d37c5455de;hp=c18a8a2355bdb0712f03e97c16b10e42f0b148ed;hpb=a35bdf653fe2f56b6600c57f53991a0191cb0032;p=jalview.git
diff --git a/src/jalview/gui/structurechooser/StructureChooserQuerySource.java b/src/jalview/gui/structurechooser/StructureChooserQuerySource.java
index c18a8a2..cdf0d57 100644
--- a/src/jalview/gui/structurechooser/StructureChooserQuerySource.java
+++ b/src/jalview/gui/structurechooser/StructureChooserQuerySource.java
@@ -1,5 +1,27 @@
+/*
+ * 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.gui.structurechooser;
+import java.util.Locale;
+
import java.util.Collection;
import java.util.List;
import java.util.Objects;
@@ -42,7 +64,7 @@ public abstract class StructureChooserQuerySource
public static StructureChooserQuerySource getPDBfts()
{
- return new PDBStructureChooserQuerySource();
+ return new PDBStructureChooserQuerySource();
}
public static StructureChooserQuerySource getTDBfts()
@@ -65,7 +87,6 @@ public abstract class StructureChooserQuerySource
return docFieldPrefs;
}
-
/**
* Builds a query string for a given sequences using its DBRef entries
*
@@ -75,7 +96,6 @@ public abstract class StructureChooserQuerySource
*/
public abstract String buildQuery(SequenceI seq);
-
/**
* Remove the following special characters from input string +, -, &, !, (, ),
@@ -110,7 +130,7 @@ public abstract class StructureChooserQuerySource
{
return false;
}
- seqName = seqName.toLowerCase();
+ seqName = seqName.toLowerCase(Locale.ROOT);
for (String ignoredEntry : ignoreList.split(","))
{
if (seqName.contains(ignoredEntry))
@@ -167,7 +187,8 @@ public abstract class StructureChooserQuerySource
*
* @param seq
* - seq to generate a query for
- * @param discoveredStructuresSet - existing set of entries - allows client side selection
+ * @param discoveredStructuresSet
+ * - existing set of entries - allows client side selection
* @param wantedFields
* - fields to retrieve
* @param selectedFilterOpt
@@ -178,7 +199,8 @@ public abstract class StructureChooserQuerySource
* @throws Exception
*/
public abstract FTSRestResponse selectFirstRankedQuery(SequenceI seq,
- Collection discoveredStructuresSet, Collection wantedFields, String fieldToFilterBy,
+ Collection discoveredStructuresSet,
+ Collection wantedFields, String fieldToFilterBy,
boolean b) throws Exception;
/**
@@ -200,15 +222,17 @@ public abstract class StructureChooserQuerySource
/**
* @param VIEWS_FILTER
- * - a String key that can be used by the caller to tag the returned filter
- * options to distinguish them in a collection
+ * - a String key that can be used by the caller to tag the returned
+ * filter options to distinguish them in a collection
* @return list of FilterOption - convention is that the last one in the list
* will be constructed with 'addSeparator==true'
*/
- public abstract List getAvailableFilterOptions(String VIEWS_FILTER);
+ public abstract List getAvailableFilterOptions(
+ String VIEWS_FILTER);
/**
* construct a structure chooser query source for the given set of sequences
+ *
* @param selectedSeqs
* @return PDBe or 3DB query source
*/
@@ -216,22 +240,44 @@ public abstract class StructureChooserQuerySource
SequenceI[] selectedSeqs)
{
ThreeDBStructureChooserQuerySource tdbSource = new ThreeDBStructureChooserQuerySource();
- boolean hasUniprot=false;
- boolean hasNA=false,hasProtein=false;
- for (SequenceI seq:selectedSeqs)
+ boolean hasUniprot = false, hasCanonical = false;
+ boolean hasNA = false, hasProtein = false;
+ int protWithoutUni = 0;
+ int protWithoutCanon = 0;
+ for (SequenceI seq : selectedSeqs)
{
- hasNA|=!seq.isProtein();
+ hasNA |= !seq.isProtein();
hasProtein |= seq.isProtein();
if (seq.isProtein())
{
- String query = tdbSource.buildQuery(seq);
- if (query!=null && query.length()>0)
+ int refsAvailable = ThreeDBStructureChooserQuerySource
+ .checkUniprotRefs(seq.getDBRefs());
+ if (refsAvailable > -2)
{
- hasUniprot=true;
+ if (refsAvailable > -1)
+ {
+ hasCanonical = true;
+ }
+ else
+ {
+ protWithoutCanon++;
+ }
+ hasUniprot = true;
+ }
+ else
+ {
+ protWithoutUni++;
+
}
}
}
- if (hasProtein && hasUniprot && !hasNA)
+ //
+ // logic: all canonicals - no fetchdb
+ // some uniprot no canonicals: defer to PDB, user can optionally fetch
+ //
+ if (hasProtein && hasCanonical && !hasNA && protWithoutCanon == 0
+ && protWithoutUni == 0)
+
{
return tdbSource;
}
@@ -239,10 +285,17 @@ public abstract class StructureChooserQuerySource
}
/**
- * some filter options may mean the original query needs to be executed again.
+ * some filter options may mean the original query needs to be executed again.
+ *
* @param selectedFilterOpt
* @return true if the fetchStructuresMetadata method needs to be called again
*/
public abstract boolean needsRefetch(FilterOption selectedFilterOpt);
+ public void updateAvailableFilterOptions(String VIEWS_FILTER,
+ List xtantOptions, Collection lastFTSData)
+ {
+ // TODO Auto-generated method stub
+
+ }
}
\ No newline at end of file