X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fuimodel%2FPDBRestResponse.java;fp=src%2Fjalview%2Fws%2Fuimodel%2FPDBRestResponse.java;h=0000000000000000000000000000000000000000;hb=64dd25185d2caf389946bb7e70053183d5aa31a6;hp=3471fab0ae4e8e233df672a38c21630b82b6ac4d;hpb=39a3725d4d499eb0f1bd14e3c049cd954faddfdc;p=jalview.git

diff --git a/src/jalview/ws/uimodel/PDBRestResponse.java b/src/jalview/ws/uimodel/PDBRestResponse.java
deleted file mode 100644
index 3471fab..0000000
--- a/src/jalview/ws/uimodel/PDBRestResponse.java
+++ /dev/null
@@ -1,314 +0,0 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 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 <http://www.gnu.org/licenses/>.
- * The Jalview Authors are detailed in the 'AUTHORS' file.
- */
-
-package jalview.ws.uimodel;
-
-import jalview.datamodel.SequenceI;
-import jalview.ws.dbsources.PDBRestClient.PDBDocField;
-import jalview.ws.dbsources.PDBRestClient.PDBDocField.Group;
-
-import java.util.Collection;
-import java.util.Objects;
-
-import javax.swing.JTable;
-import javax.swing.table.DefaultTableModel;
-
-import org.json.simple.JSONObject;
-
-/**
- * Represents the response model produced by the PDBRestClient upon successful
- * execution of a given request
- * 
- * @author tcnofoegbu
- *
- */
-public class PDBRestResponse
-{
-  private int numberOfItemsFound;
-
-  private String responseTime;
-
-  private Collection<PDBResponseSummary> searchSummary;
-
-  public int getNumberOfItemsFound()
-  {
-    return numberOfItemsFound;
-  }
-
-  public void setNumberOfItemsFound(int itemFound)
-  {
-    this.numberOfItemsFound = itemFound;
-  }
-
-  public String getResponseTime()
-  {
-    return responseTime;
-  }
-
-  public void setResponseTime(String responseTime)
-  {
-    this.responseTime = responseTime;
-  }
-
-  public Collection<PDBResponseSummary> getSearchSummary()
-  {
-    return searchSummary;
-  }
-
-  public void setSearchSummary(Collection<PDBResponseSummary> searchSummary)
-  {
-    this.searchSummary = searchSummary;
-  }
-
-  /**
-   * Convenience method to obtain a Table model for a given summary List based
-   * on the request parameters
-   * 
-   * @param request
-   *          the PDBRestRequest object which holds useful information for
-   *          creating a table model
-   * @param summariesList
-   *          the summary list which contains the data for populating the
-   *          table's rows
-   * @return the table model which was dynamically generated
-   */
-  public static DefaultTableModel getTableModel(PDBRestRequest request,
-          Collection<PDBResponseSummary> summariesList)
-  {
-    final PDBDocField[] cols = request.getWantedFields().toArray(
-            new PDBDocField[0]);
-    final int colOffset = request.getAssociatedSequence() == null ? 0 : 1;
-    DefaultTableModel tableModel = new DefaultTableModel()
-    {
-      @Override
-      public boolean isCellEditable(int row, int column)
-      {
-        return false;
-      }
-
-      @Override
-      public Class<?> getColumnClass(int columnIndex)
-      {
-        if (colOffset == 1 && columnIndex == 0)
-        {
-          return String.class;
-        }
-        if (cols[columnIndex - colOffset].getGroup().getName()
-                .equalsIgnoreCase(Group.QUALITY_MEASURES.getName()))
-        {
-          return Double.class;
-        }
-        return String.class;
-      }
-
-    };
-    if (request.getAssociatedSequence() != null)
-    {
-      tableModel.addColumn("Ref Sequence"); // Create sequence column header if
-      // exists in the request
-    }
-    for (PDBDocField field : request.getWantedFields())
-    {
-      tableModel.addColumn(field.getName()); // Create sequence column header if
-                                             // exists in the request
-    }
-
-    for (PDBResponseSummary res : summariesList)
-    {
-      tableModel.addRow(res.getSummaryData()); // Populate table rows with
-                                               // summary list
-    }
-
-    return tableModel;
-  }
-
-  /**
-   * Model for a unique response summary
-   * 
-   */
-  public class PDBResponseSummary
-  {
-    private String pdbId;
-
-    private Object[] summaryRowData;
-
-    private SequenceI associatedSequence;
-
-    public PDBResponseSummary(JSONObject pdbJsonDoc, PDBRestRequest request)
-    {
-      Collection<PDBDocField> diplayFields = request.getWantedFields();
-      SequenceI associatedSeq = request.getAssociatedSequence();
-      int colCounter = 0;
-      summaryRowData = new Object[(associatedSeq != null) ? diplayFields
-              .size() + 1 : diplayFields.size()];
-      if (associatedSeq != null)
-      {
-        this.associatedSequence = associatedSeq;
-        summaryRowData[0] = associatedSequence;
-        colCounter = 1;
-      }
-
-      for (PDBDocField field : diplayFields)
-      {
-        String fieldData = (pdbJsonDoc.get(field.getCode()) == null) ? ""
-                : pdbJsonDoc.get(field.getCode()).toString();
-        if (field.equals(PDBDocField.PDB_ID))
-        {
-          this.pdbId = fieldData;
-          summaryRowData[colCounter++] = this.pdbId;
-        }
-        else
-        {
-          if (field.getGroup().getName()
-                  .equals(Group.QUALITY_MEASURES.getName()))
-          {
-            try
-            {
-              if (fieldData == null || fieldData.isEmpty())
-              {
-                summaryRowData[colCounter++] = null;
-              }
-              else
-              {
-              Double value = Double.valueOf(fieldData);
-              summaryRowData[colCounter++] = value;
-              }
-            } catch (Exception e)
-            {
-              e.printStackTrace();
-              System.out.println("offending value:" + fieldData);
-              summaryRowData[colCounter++] = 0.0;
-            }
-          }else{
-            summaryRowData[colCounter++] = (fieldData == null || fieldData
-                    .isEmpty()) ? null : fieldData;
-          }
-        }
-      }
-    }
-
-    public Object getPdbId()
-    {
-      return pdbId;
-    }
-
-    public void setPdbId(String pdbId)
-    {
-      this.pdbId = pdbId;
-    }
-
-    public Object[] getSummaryData()
-    {
-      return summaryRowData;
-    }
-
-    public void setSummaryData(Object[] summaryData)
-    {
-      this.summaryRowData = summaryData;
-    }
-
-    /**
-     * Returns a string representation of this object;
-     */
-    @Override
-    public String toString()
-    {
-      StringBuilder summaryFieldValues = new StringBuilder();
-      for (Object summaryField : summaryRowData)
-      {
-        summaryFieldValues.append(
-                summaryField == null ? " " : summaryField.toString())
-                .append("\t");
-      }
-      return summaryFieldValues.toString();
-    }
-
-    /**
-     * Returns hash code value for this object
-     */
-    @Override
-    public int hashCode()
-    {
-      return Objects.hash(this.pdbId, this.toString());
-    }
-
-    /**
-     * Indicates whether some object is equal to this one
-     */
-    @Override
-    public boolean equals(Object that)
-    {
-      if (!(that instanceof PDBResponseSummary))
-      {
-        return false;
-      }
-      PDBResponseSummary another = (PDBResponseSummary) that;
-      return this.toString().equals(another.toString());
-    }
-
-  }
-
-  public static void configureTableColumn(JTable tbl_summary,
-          Collection<PDBDocField> wantedFields)
-  {
-    try
-    {
-      // wait for table model initialisation to complete
-      Thread.sleep(1200);
-    } catch (InterruptedException e1)
-    {
-      e1.printStackTrace();
-    }
-    for (PDBDocField wantedField : wantedFields)
-    {
-      try
-      {
-      if (wantedField.equals(PDBDocField.PDB_ID))
-      {
-        tbl_summary.getColumn(wantedField.getName()).setMinWidth(40);
-        tbl_summary.getColumn(wantedField.getName()).setMaxWidth(60);
-        tbl_summary.getColumn(wantedField.getName()).setPreferredWidth(45);
-      }
-      else if (wantedField.equals(PDBDocField.TITLE))
-      {
-        tbl_summary.getColumn(wantedField.getName()).setMinWidth(300);
-        tbl_summary.getColumn(wantedField.getName()).setMaxWidth(1000);
-        tbl_summary.getColumn(wantedField.getName()).setPreferredWidth(400);
-      }
-      else if (wantedField.getGroup() == Group.QUALITY_MEASURES)
-      {
-        tbl_summary.getColumn(wantedField.getName()).setMinWidth(50);
-        tbl_summary.getColumn(wantedField.getName()).setMaxWidth(150);
-        tbl_summary.getColumn(wantedField.getName()).setPreferredWidth(85);
-      }
-      else
-      {
-        tbl_summary.getColumn(wantedField.getName()).setMinWidth(50);
-        tbl_summary.getColumn(wantedField.getName()).setMaxWidth(400);
-        tbl_summary.getColumn(wantedField.getName()).setPreferredWidth(95);
-      }
-      } catch (Exception e)
-      {
-        e.printStackTrace();
-      }
-    }
-  }
-}