JAL-3829 3d-beacons structure chooser logic (not yet finished)

[jalview.git] / src / jalview / gui / structurechooser / StructureChooserQuerySource.java

diff --git a/src/jalview/gui/structurechooser/StructureChooserQuerySource.java b/src/jalview/gui/structurechooser/StructureChooserQuerySource.java
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+++ b/src/jalview/gui/structurechooser/StructureChooserQuerySource.java
@@ -0,0 +1,207 @@
+package jalview.gui.structurechooser;
+
+import java.util.Collection;
+import java.util.HashSet;
+import java.util.LinkedHashSet;
+import java.util.List;
+import java.util.Objects;
+import java.util.Set;
+import java.util.Vector;
+
+import javax.swing.JTable;
+import javax.swing.table.TableModel;
+
+import jalview.datamodel.DBRefEntry;
+import jalview.datamodel.DBRefSource;
+import jalview.datamodel.PDBEntry;
+import jalview.datamodel.SequenceI;
+import jalview.fts.api.FTSData;
+import jalview.fts.api.FTSDataColumnI;
+import jalview.fts.api.FTSRestClientI;
+import jalview.fts.core.FTSDataColumnPreferences;
+import jalview.fts.core.FTSDataColumnPreferences.PreferenceSource;
+import jalview.fts.core.FTSRestRequest;
+import jalview.fts.core.FTSRestResponse;
+import jalview.fts.service.pdb.PDBFTSRestClient;
+import jalview.jbgui.GStructureChooser.FilterOption;
+
+/**
+ * logic for querying sources of structural data for structures of sequences
+ * 
+ * @author jprocter
+ *
+ * @param <T>
+ */
+public abstract class StructureChooserQuerySource
+{
+  protected FTSRestRequest lastPdbRequest;
+
+  protected FTSRestClientI pdbRestClient;
+
+  protected FTSDataColumnPreferences docFieldPrefs;
+
+  /**
+   * max length of a GET URL (probably :( )
+   */
+  protected static int MAX_QLENGTH = 7820;
+
+  public StructureChooserQuerySource()
+  {
+  }
+
+  public static StructureChooserQuerySource getPDBfts()
+  {
+          return new PDBStructureChooserQuerySource();
+  }
+
+  public static StructureChooserQuerySource getTDBfts()
+  {
+    return new ThreeDBStructureChooserQuerySource();
+  }
+
+  public FTSDataColumnPreferences getDocFieldPrefs()
+  {
+    return docFieldPrefs;
+  }
+
+  public void setDocFieldPrefs(FTSDataColumnPreferences docFieldPrefs)
+  {
+    this.docFieldPrefs = docFieldPrefs;
+  }
+
+  public FTSDataColumnPreferences getInitialFieldPreferences()
+  {
+    return docFieldPrefs;
+  }
+
+
+  /**
+   * Builds a query string for a given sequences using its DBRef entries
+   * 
+   * @param seq
+   *          the sequences to build a query for
+   * @return the built query string
+   */
+
+  public abstract String buildQuery(SequenceI seq);
+  
+
+  /**
+   * Remove the following special characters from input string +, -, &, !, (, ),
+   * {, }, [, ], ^, ", ~, *, ?, :, \
+   * 
+   * @param seqName
+   * @return
+   */
+  public static String sanitizeSeqName(String seqName)
+  {
+    Objects.requireNonNull(seqName);
+    return seqName.replaceAll("\\[\\d*\\]", "")
+            .replaceAll("[^\\dA-Za-z|_]", "").replaceAll("\\s+", "+");
+  }
+
+  /**
+   * Ensures sequence ref names are not less than 3 characters and does not
+   * contain a database name
+   * 
+   * @param seqName
+   * @return
+   */
+  static boolean isValidSeqName(String seqName)
+  {
+    // System.out.println("seqName : " + seqName);
+    String ignoreList = "pdb,uniprot,swiss-prot";
+    if (seqName.length() < 3)
+    {
+      return false;
+    }
+    if (seqName.contains(":"))
+    {
+      return false;
+    }
+    seqName = seqName.toLowerCase();
+    for (String ignoredEntry : ignoreList.split(","))
+    {
+      if (seqName.contains(ignoredEntry))
+      {
+        return false;
+      }
+    }
+    return true;
+  }
+
+  static String getDBRefId(DBRefEntry dbRef)
+  {
+    String ref = dbRef.getAccessionId().replaceAll("GO:", "");
+    return ref;
+  }
+
+  static PDBEntry getFindEntry(String id, Vector<PDBEntry> pdbEntries)
+  {
+    Objects.requireNonNull(id);
+    Objects.requireNonNull(pdbEntries);
+    PDBEntry foundEntry = null;
+    for (PDBEntry entry : pdbEntries)
+    {
+      if (entry.getId().equalsIgnoreCase(id))
+      {
+        return entry;
+      }
+    }
+    return foundEntry;
+  }
+
+  /**
+   * FTSRestClient specific query builder to recover associated structure data
+   * records for a sequence
+   * 
+   * @param seq
+   *          - seq to generate a query for
+   * @param wantedFields
+   *          - fields to retrieve
+   * @param selectedFilterOpt
+   *          - criterion for ranking results (e.g. resolution)
+   * @param b
+   *          - sort ascending or descending
+   * @return
+   * @throws Exception
+   */
+  public abstract FTSRestResponse fetchStructuresMetaData(SequenceI seq,
+          Collection<FTSDataColumnI> wantedFields,
+          FilterOption selectedFilterOpt, boolean b) throws Exception;
+
+  /**
+   * FTSRestClient specific query builder to pick top ranked entry from a
+   * fetchStructuresMetaData query
+   * 
+   * @param seq
+   *          - seq to generate a query for
+   * @param wantedFields
+   *          - fields to retrieve
+   * @param selectedFilterOpt
+   *          - criterion for ranking results (e.g. resolution)
+   * @param b
+   *          - sort ascending or descending
+   * @return
+   * @throws Exception
+   */
+  public abstract FTSRestResponse selectFirstRankedQuery(SequenceI seq,
+          Collection<FTSDataColumnI> wantedFields, String fieldToFilterBy,
+          boolean b) throws Exception;
+
+  /**
+   * 
+   * @param discoveredStructuresSet
+   * @return the table model for the given result set for this engine
+   */
+  public TableModel getTableModel(
+          Collection<FTSData> discoveredStructuresSet)
+  {
+    return FTSRestResponse.getTableModel(lastPdbRequest,
+            discoveredStructuresSet);
+  }
+
+  public abstract PDBEntry[] collectSelectedRows(JTable restable,
+          int[] selectedRows, List<SequenceI> selectedSeqsToView);
+
+}
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