+++ /dev/null
-/*
- * 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();
- }
- }
- }
-}
git://source.jalview.org / jalview.git / blobdiff