X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2Fstructurechooser%2FTDBResultAnalyser.java;h=e817b26bc8d18cfc4bc8934f1b60a66a949b2270;hb=a6f0678764ea06034460236c7a811bbfcad682aa;hp=9f571006c1d8263998dd02d4650c83f99a72ab4c;hpb=9018c06add8548b4921a4c21f21a1b85a0bea1de;p=jalview.git
diff --git a/src/jalview/gui/structurechooser/TDBResultAnalyser.java b/src/jalview/gui/structurechooser/TDBResultAnalyser.java
index 9f57100..e817b26 100644
--- a/src/jalview/gui/structurechooser/TDBResultAnalyser.java
+++ b/src/jalview/gui/structurechooser/TDBResultAnalyser.java
@@ -1,3 +1,23 @@
+/*
+ * 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.ArrayList;
@@ -7,6 +27,7 @@ import java.util.Collection;
import java.util.Collections;
import java.util.Comparator;
import java.util.List;
+import java.util.Locale;
import jalview.datamodel.SequenceI;
import jalview.fts.api.FTSData;
@@ -23,8 +44,8 @@ public class TDBResultAnalyser
*/
private static List EXP_CATEGORIES = Arrays
.asList(new String[]
- { "EXPERIMENTALLY DETERMINED", "DEEP-LEARNING", "TEMPLATE-BASED",
- "AB-INITIO", "CONFORMATIONAL ENSEMBLE" });
+ { "EXPERIMENTALLY DETERMINED", "DEEP-LEARNING", "AB-INITIO",
+ "TEMPLATE-BASED", "CONFORMATIONAL ENSEMBLE" });
private SequenceI seq;
@@ -40,6 +61,8 @@ public class TDBResultAnalyser
private int idx_mqual;
+ private int idx_mqualtype;
+
private int idx_resol;
/**
@@ -70,6 +93,7 @@ public class TDBResultAnalyser
idx_mprov = lastTdbRequest.getFieldIndex("Provider");
idx_mqual = lastTdbRequest.getFieldIndex("Confidence");
idx_resol = lastTdbRequest.getFieldIndex("Resolution");
+ idx_mqualtype = lastTdbRequest.getFieldIndex("Confidence Score Type");
}
/**
@@ -85,7 +109,7 @@ public class TDBResultAnalyser
{
return 0;
}
- String upper_cat = cat.toUpperCase();
+ String upper_cat = cat.toUpperCase(Locale.ROOT);
int idx = EXP_CATEGORIES.indexOf(upper_cat);
if (idx == -1)
{
@@ -109,18 +133,22 @@ public class TDBResultAnalyser
// ignore anything outside the sequence region
for (FTSData row : collectedResults)
{
- int up_s = (Integer) row.getSummaryData()[idx_ups];
- int up_e = (Integer) row.getSummaryData()[idx_upe];
- String provider = (String) row.getSummaryData()[idx_mprov];
- String mcat = (String) row.getSummaryData()[idx_mcat];
- // this makes sure all new categories are in the score array.
- int scorecat = scoreCategory(mcat);
- if (sourceFilter == null || sourceFilter.equals(provider))
+ if (row.getSummaryData() != null
+ && row.getSummaryData()[idx_ups] != null)
{
- if (seq == row.getSummaryData()[0] && up_e > seq.getStart()
- && up_s < seq.getEnd())
+ int up_s = (Integer) row.getSummaryData()[idx_ups];
+ int up_e = (Integer) row.getSummaryData()[idx_upe];
+ String provider = (String) row.getSummaryData()[idx_mprov];
+ String mcat = (String) row.getSummaryData()[idx_mcat];
+ // this makes sure all new categories are in the score array.
+ int scorecat = scoreCategory(mcat);
+ if (sourceFilter == null || sourceFilter.equals(provider))
{
- filteredResponse.add(row);
+ if (seq == row.getSummaryData()[0] && up_e > seq.getStart()
+ && up_s < seq.getEnd())
+ {
+ filteredResponse.add(row);
+ }
}
}
}
@@ -136,12 +164,15 @@ public class TDBResultAnalyser
int o1_s = (Integer) o1data[idx_ups];
int o1_e = (Integer) o1data[idx_upe];
int o1_cat = scoreCategory((String) o1data[idx_mcat]);
- String o1_prov= ((String) o1data[idx_mprov]).toUpperCase();
+ String o1_prov = ((String) o1data[idx_mprov])
+ .toUpperCase(Locale.ROOT);
int o2_s = (Integer) o2data[idx_ups];
int o2_e = (Integer) o2data[idx_upe];
int o2_cat = scoreCategory((String) o2data[idx_mcat]);
- String o2_prov= ((String) o2data[idx_mprov]).toUpperCase();
-
+ String o2_prov = ((String) o2data[idx_mprov])
+ .toUpperCase(Locale.ROOT);
+ String o1_qualtype = (String) o1data[idx_mqualtype],
+ o2_qualtype = (String) o2data[idx_mqualtype];
if (o1_cat == o2_cat)
{
@@ -151,29 +182,53 @@ public class TDBResultAnalyser
int o2_xtent = o2_e - o2_s;
if (o1_xtent == o2_xtent)
{
+ // EXPERIMENTAL DATA ALWAYS TRUMPS MODELS
if (o1_cat == scoreCategory(EXP_CATEGORIES.get(0)))
{
- if (o1_prov.equals(o2_prov)) {
- if ("PDBE".equals(o1_prov)) {
- if (eitherNull(idx_resol,o1data,o2data))
+ if (o1_prov.equals(o2_prov))
+ {
+ if ("PDBE".equals(o1_prov))
+ {
+ if (eitherNull(idx_resol, o1data, o2data))
{
- return nonNullFirst(idx_resol,o1data,o2data);
+ return nonNullFirst(idx_resol, o1data, o2data);
}
- // experimental structures, so rank on quality
- double o1_res = (Double) o1data[idx_resol];
- double o2_res = (Double) o2data[idx_resol];
- return (o2_res < o1_res) ? 1 : (o2_res == o1_res) ? 0 : -1;
- } else {
- return 0; // no change in order
+ // experimental structures, so rank on quality
+ double o1_res = (Double) o1data[idx_resol];
+ double o2_res = (Double) o2data[idx_resol];
+ return (o2_res < o1_res) ? 1
+ : (o2_res == o1_res) ? 0 : -1;
+ }
+ else
+ {
+ return 0; // no change in order
+ }
+ }
+ else
+ {
+ // PDBe always ranked above all other experimentally
+ // determined categories
+ return "PDBE".equals(o1_prov) ? -1
+ : "PDBE".equals(o2_prov) ? 1 : 0;
}
- } else {
- // PDBe always ranked above all other experimentally determined categories
- return "PDBE".equals(o1_prov) ? -1 : "PDBE".equals(o2_prov) ? 1 : 0;
- }
}
else
{
- if (eitherNull(idx_mqual,o1data, o2data)) {
+ // RANK ON QUALITY - DOWNRANK THOSE WITH NO QUALITY MEASURE
+ if (eitherNull(idx_mqualtype, o1data, o2data))
+ {
+ return nonNullFirst(idx_mqualtype, o1data, o2data);
+ }
+ // ONLY COMPARE LIKE QUALITY SCORES
+ if (!o1_qualtype.equals(o2_qualtype))
+ {
+ // prefer LDDT measure over others
+ return "pLDDT".equals(o1_prov) ? -1
+ : "pLDDT".equals(o2_prov) ? 1 : 0;
+ }
+ // OR NO VALUE FOR THE QUALITY
+ if (eitherNull(idx_mqual, o1data, o2data))
+ {
return nonNullFirst(idx_mqual, o1data, o2data);
}
// models, so rank on qmean - b
@@ -194,6 +249,12 @@ public class TDBResultAnalyser
}
else
{
+ // if both are not experimental, then favour alphafold
+ if (o2_cat > 0 && o1_cat > 0)
+ {
+ return "ALPHAFOLD DB".equals(o1_prov) ? -1
+ : "ALPHAFOLD DB".equals(o2_prov) ? 1 : 0;
+ }
return o2_cat - o1_cat;
}
}
@@ -201,13 +262,14 @@ public class TDBResultAnalyser
private int nonNullFirst(int idx_resol, Object[] o1data,
Object[] o2data)
{
- return o1data[idx_resol] == o2data[idx_resol] ? 0: o1data[idx_resol] != null ? -1 : 1;
+ return o1data[idx_resol] == o2data[idx_resol] ? 0
+ : o1data[idx_resol] != null ? -1 : 1;
}
private boolean eitherNull(int idx_resol, Object[] o1data,
Object[] o2data)
{
- return (o1data[idx_resol] == null || o2data[idx_resol]==null);
+ return (o1data[idx_resol] == null || o2data[idx_resol] == null);
}
@Override
@@ -233,6 +295,8 @@ public class TDBResultAnalyser
BitSet cover = new BitSet();
cover.set(seq.getStart(), seq.getEnd());
// walk down the list of structures, selecting some to add to selected
+ // TODO: could do simple DP - double loop to select largest number of
+ // structures covering largest number of sites
for (FTSData structure : filteredStructures)
{
Object[] odata = structure.getSummaryData();
@@ -250,7 +314,7 @@ public class TDBResultAnalyser
cover.andNot(scover);
}
}
- if (selected.size()==0)
+ if (selected.size() == 0)
{
return selected;
}