/*
 * 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 <http://www.gnu.org/licenses/>.
 * The Jalview Authors are detailed in the 'AUTHORS' file.
 */
package jalview.gui;

import static org.testng.Assert.assertEquals;
import static org.testng.Assert.assertTrue;

import jalview.api.AlignViewportI;
import jalview.bin.Cache;
import jalview.bin.Jalview;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceI;
import jalview.gui.SeqPanel.MousePos;
import jalview.io.DataSourceType;
import jalview.io.FileLoader;

import java.awt.Event;
import java.awt.event.MouseEvent;

import org.testng.annotations.AfterMethod;
import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;

public class SeqPanelTest
{
  AlignFrame af;

  @BeforeClass(alwaysRun = true)
  public void setUpJvOptionPane()
  {
    JvOptionPane.setInteractiveMode(false);
    JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
  }
  @Test(groups = "Functional")
  public void testSetStatusReturnsNearestResiduePosition()
  {
    SequenceI seq1 = new Sequence("Seq1", "AACDE");
    SequenceI seq2 = new Sequence("Seq2", "AA--E");
    AlignmentI al = new Alignment(new SequenceI[] { seq1, seq2 });
    AlignFrame alignFrame = new AlignFrame(al, al.getWidth(),
            al.getHeight());
    AlignmentI visAl = alignFrame.getViewport().getAlignment();

    // Test either side of gap
    assertEquals(
            alignFrame.alignPanel.getSeqPanel().setStatusMessage(
                    visAl.getSequenceAt(1), 1, 1), 2);
    assertEquals(alignFrame.statusBar.getText(),
            "Sequence 2 ID: Seq2 Residue: ALA (2)");
    assertEquals(
            alignFrame.alignPanel.getSeqPanel().setStatusMessage(
                    visAl.getSequenceAt(1), 4, 1), 3);
    assertEquals(alignFrame.statusBar.getText(),
            "Sequence 2 ID: Seq2 Residue: GLU (3)");
    // no status message at a gap, returns next residue position to the right
    assertEquals(
            alignFrame.alignPanel.getSeqPanel().setStatusMessage(
                    visAl.getSequenceAt(1), 2, 1), 3);
    assertEquals(alignFrame.statusBar.getText(), "Sequence 2 ID: Seq2");
    assertEquals(
            alignFrame.alignPanel.getSeqPanel().setStatusMessage(
                    visAl.getSequenceAt(1), 3, 1), 3);
    assertEquals(alignFrame.statusBar.getText(), "Sequence 2 ID: Seq2");
  }

  @Test(groups = "Functional")
  public void testAmbiguousAminoAcidGetsStatusMessage()
  {
    SequenceI seq1 = new Sequence("Seq1", "ABCDE");
    SequenceI seq2 = new Sequence("Seq2", "AB--E");
    AlignmentI al = new Alignment(new SequenceI[] { seq1, seq2 });
    AlignFrame alignFrame = new AlignFrame(al, al.getWidth(),
            al.getHeight());
    AlignmentI visAl = alignFrame.getViewport().getAlignment();

    assertEquals(
            alignFrame.alignPanel.getSeqPanel().setStatusMessage(
                    visAl.getSequenceAt(1), 1, 1), 2);
    assertEquals(alignFrame.statusBar.getText(),
            "Sequence 2 ID: Seq2 Residue: B (2)");
  }

  @Test(groups = "Functional")
  public void testFindMousePosition_unwrapped()
  {
    String seqData = ">Seq1\nAACDE\n>Seq2\nAA--E\n";
    AlignFrame alignFrame = new FileLoader().LoadFileWaitTillLoaded(seqData,
            DataSourceType.PASTE);
    AlignViewportI av = alignFrame.getViewport();
    av.setShowAnnotation(true);
    av.setWrapAlignment(false);
    final int charHeight = av.getCharHeight();
    final int charWidth = av.getCharWidth();
    // sanity checks:
    assertTrue(charHeight > 0);
    assertTrue(charWidth > 0);
    assertTrue(alignFrame.alignPanel.getSeqPanel().getWidth() > 0);

    SeqPanel testee = alignFrame.alignPanel.getSeqPanel();
    int x = 0;
    int y = 0;

    /*
     * mouse at top left of unwrapped panel
     */
    MouseEvent evt = new MouseEvent(testee, Event.MOUSE_MOVE, 0L, 0, x, y,
            0, 0, 0, false, 0);
    MousePos pos = testee.findMousePosition(evt);
    assertEquals(pos.column, 0);
    assertEquals(pos.seqIndex, 0);
    assertEquals(pos.annotationIndex, -1);
  }

  @AfterMethod(alwaysRun = true)
  public void tearDown()
  {
    Desktop.instance.closeAll_actionPerformed(null);
  }

  @Test(groups = "Functional")
  public void testFindMousePosition_wrapped()
  {
    Cache.applicationProperties.setProperty("SHOW_ANNOTATIONS", "true");
    Cache.applicationProperties.setProperty("WRAP_ALIGNMENT", "true");
    AlignFrame alignFrame = new FileLoader().LoadFileWaitTillLoaded(
            "examples/uniref50.fa", DataSourceType.FILE);
    AlignViewportI av = alignFrame.getViewport();
    av.setScaleAboveWrapped(false);
    av.setScaleLeftWrapped(false);
    av.setScaleRightWrapped(false);
    alignFrame.alignPanel.paintAlignment(false, false);

    final int charHeight = av.getCharHeight();
    final int charWidth = av.getCharWidth();
    final int alignmentHeight = av.getAlignment().getHeight();
    
    // sanity checks:
    assertTrue(charHeight > 0);
    assertTrue(charWidth > 0);
    assertTrue(alignFrame.alignPanel.getSeqPanel().getWidth() > 0);
  
    SeqPanel testee = alignFrame.alignPanel.getSeqPanel();
    int x = 0;
    int y = 0;
  
    /*
     * mouse at top left of wrapped panel; there is a gap of charHeight
     * above the alignment
     */
    MouseEvent evt = new MouseEvent(testee, Event.MOUSE_MOVE, 0L, 0, x, y,
            0, 0, 0, false, 0);
    MousePos pos = testee.findMousePosition(evt);
    assertEquals(pos.column, 0);
    assertEquals(pos.seqIndex, -1); // above sequences
    assertEquals(pos.annotationIndex, -1);

    /*
     * cursor at bottom of gap above
     */
    y = charHeight - 1;
    evt = new MouseEvent(testee, Event.MOUSE_MOVE, 0L, 0, x, y, 0, 0, 0,
            false, 0);
    pos = testee.findMousePosition(evt);
    assertEquals(pos.seqIndex, -1);
    assertEquals(pos.annotationIndex, -1);

    /*
     * cursor over top of first sequence
     */
    y = charHeight;
    evt = new MouseEvent(testee, Event.MOUSE_MOVE, 0L, 0, x, y, 0, 0, 0,
            false, 0);
    pos = testee.findMousePosition(evt);
    assertEquals(pos.seqIndex, 0);
    assertEquals(pos.annotationIndex, -1);

    /*
     * cursor at bottom of first sequence
     */
    y = 2 * charHeight - 1;
    evt = new MouseEvent(testee, Event.MOUSE_MOVE, 0L, 0, x, y, 0, 0, 0,
            false, 0);
    pos = testee.findMousePosition(evt);
    assertEquals(pos.seqIndex, 0);
    assertEquals(pos.annotationIndex, -1);

    /*
     * cursor at top of second sequence
     */
    y = 2 * charHeight;
    evt = new MouseEvent(testee, Event.MOUSE_MOVE, 0L, 0, x, y, 0, 0, 0,
            false, 0);
    pos = testee.findMousePosition(evt);
    assertEquals(pos.seqIndex, 1);
    assertEquals(pos.annotationIndex, -1);

    /*
     * cursor at bottom of second sequence
     */
    y = 3 * charHeight - 1;
    evt = new MouseEvent(testee, Event.MOUSE_MOVE, 0L, 0, x, y, 0, 0, 0,
            false, 0);
    pos = testee.findMousePosition(evt);
    assertEquals(pos.seqIndex, 1);
    assertEquals(pos.annotationIndex, -1);

    /*
     * cursor at bottom of last sequence
     */
    y = charHeight * (1 + alignmentHeight) - 1;
    evt = new MouseEvent(testee, Event.MOUSE_MOVE, 0L, 0, x, y, 0, 0, 0,
            false, 0);
    pos = testee.findMousePosition(evt);
    assertEquals(pos.seqIndex, alignmentHeight - 1);
    assertEquals(pos.annotationIndex, -1);

    /*
     * cursor below sequences, in 3-pixel gap above annotations
     */
    y += 1;
    evt = new MouseEvent(testee, Event.MOUSE_MOVE, 0L, 0, x, y, 0, 0, 0,
            false, 0);
    pos = testee.findMousePosition(evt);
    assertEquals(pos.seqIndex, alignmentHeight - 1);
    assertEquals(pos.annotationIndex, -1);

    /*
     * cursor still in the gap above annotations, now at the bottom of it
     * method reports index of nearest sequence above  
     */
    y += SeqCanvas.SEQS_ANNOTATION_GAP - 1; // 3-1 = 2
    evt = new MouseEvent(testee, Event.MOUSE_MOVE, 0L, 0, x, y, 0, 0, 0,
            false, 0);
    pos = testee.findMousePosition(evt);
    assertEquals(pos.seqIndex, alignmentHeight - 1);
    assertEquals(pos.annotationIndex, -1);

    /*
     * cursor at the top of the first annotation  
     */
    y += 1;
    evt = new MouseEvent(testee, Event.MOUSE_MOVE, 0L, 0, x, y, 0, 0, 0,
            false, 0);
    pos = testee.findMousePosition(evt);
    assertEquals(pos.seqIndex, alignmentHeight - 1);
    assertEquals(pos.annotationIndex, 0); // over first annotation

    /*
     * cursor at the bottom of the first annotation  
     */
    y += av.getAlignment().getAlignmentAnnotation()[0].height - 1;
    evt = new MouseEvent(testee, Event.MOUSE_MOVE, 0L, 0, x, y, 0, 0, 0,
            false, 0);
    pos = testee.findMousePosition(evt);
    assertEquals(pos.seqIndex, alignmentHeight - 1);
    assertEquals(pos.annotationIndex, 0);

    /*
     * cursor at the top of the second annotation  
     */
    y += 1;
    evt = new MouseEvent(testee, Event.MOUSE_MOVE, 0L, 0, x, y, 0, 0, 0,
            false, 0);
    pos = testee.findMousePosition(evt);
    assertEquals(pos.seqIndex, alignmentHeight - 1);
    assertEquals(pos.annotationIndex, 1);

    /*
     * cursor at the bottom of the second annotation  
     */
    y += av.getAlignment().getAlignmentAnnotation()[1].height - 1;
    evt = new MouseEvent(testee, Event.MOUSE_MOVE, 0L, 0, x, y, 0, 0, 0,
            false, 0);
    pos = testee.findMousePosition(evt);
    assertEquals(pos.seqIndex, alignmentHeight - 1);
    assertEquals(pos.annotationIndex, 1);

    /*
     * cursor at the top of the third annotation  
     */
    y += 1;
    evt = new MouseEvent(testee, Event.MOUSE_MOVE, 0L, 0, x, y, 0, 0, 0,
            false, 0);
    pos = testee.findMousePosition(evt);
    assertEquals(pos.seqIndex, alignmentHeight - 1);
    assertEquals(pos.annotationIndex, 2);

    /*
     * cursor at the bottom of the third annotation  
     */
    y += av.getAlignment().getAlignmentAnnotation()[2].height - 1;
    evt = new MouseEvent(testee, Event.MOUSE_MOVE, 0L, 0, x, y, 0, 0, 0,
            false, 0);
    pos = testee.findMousePosition(evt);
    assertEquals(pos.seqIndex, alignmentHeight - 1);
    assertEquals(pos.annotationIndex, 2);

    /*
     * cursor in gap between wrapped widths  
     */
    y += 1;
    evt = new MouseEvent(testee, Event.MOUSE_MOVE, 0L, 0, x, y, 0, 0, 0,
            false, 0);
    pos = testee.findMousePosition(evt);
    assertEquals(pos.seqIndex, -1);
    assertEquals(pos.annotationIndex, -1);

    /*
     * cursor at bottom of gap between wrapped widths  
     */
    y += charHeight - 1;
    evt = new MouseEvent(testee, Event.MOUSE_MOVE, 0L, 0, x, y, 0, 0, 0,
            false, 0);
    pos = testee.findMousePosition(evt);
    assertEquals(pos.seqIndex, -1);
    assertEquals(pos.annotationIndex, -1);

    /*
     * cursor at top of first sequence, second wrapped width  
     */
    y += 1;
    evt = new MouseEvent(testee, Event.MOUSE_MOVE, 0L, 0, x, y, 0, 0, 0,
            false, 0);
    pos = testee.findMousePosition(evt);
    assertEquals(pos.seqIndex, 0);
    assertEquals(pos.annotationIndex, -1);
  }

  @Test(groups = "Functional")
  public void testFindMousePosition_wrapped_scaleAbove()
  {
    Cache.applicationProperties.setProperty("SHOW_ANNOTATIONS", "true");
    Cache.applicationProperties.setProperty("WRAP_ALIGNMENT", "true");
    AlignFrame alignFrame = new FileLoader().LoadFileWaitTillLoaded(
            "examples/uniref50.fa", DataSourceType.FILE);
    AlignViewportI av = alignFrame.getViewport();
    av.setScaleAboveWrapped(true);
    av.setScaleLeftWrapped(false);
    av.setScaleRightWrapped(false);
    alignFrame.alignPanel.paintAlignment(false, false);
  
    final int charHeight = av.getCharHeight();
    final int charWidth = av.getCharWidth();
    final int alignmentHeight = av.getAlignment().getHeight();
    
    // sanity checks:
    assertTrue(charHeight > 0);
    assertTrue(charWidth > 0);
    assertTrue(alignFrame.alignPanel.getSeqPanel().getWidth() > 0);
  
    SeqPanel testee = alignFrame.alignPanel.getSeqPanel();
    int x = 0;
    int y = 0;
  
    /*
     * mouse at top left of wrapped panel; there is a gap of charHeight
     * above the alignment
     */
    MouseEvent evt = new MouseEvent(testee, Event.MOUSE_MOVE, 0L, 0, x, y,
            0, 0, 0, false, 0);
    MousePos pos = testee.findMousePosition(evt);
    assertEquals(pos.column, 0);
    assertEquals(pos.seqIndex, -1); // above sequences
    assertEquals(pos.annotationIndex, -1);
  
    /*
     * cursor at bottom of gap above
     * two charHeights including scale panel
     */
    y = 2 * charHeight - 1;
    evt = new MouseEvent(testee, Event.MOUSE_MOVE, 0L, 0, x, y, 0, 0, 0,
            false, 0);
    pos = testee.findMousePosition(evt);
    assertEquals(pos.seqIndex, -1);
    assertEquals(pos.annotationIndex, -1);
  
    /*
     * cursor over top of first sequence
     */
    y += 1;
    evt = new MouseEvent(testee, Event.MOUSE_MOVE, 0L, 0, x, y, 0, 0, 0,
            false, 0);
    pos = testee.findMousePosition(evt);
    assertEquals(pos.seqIndex, 0);
    assertEquals(pos.annotationIndex, -1);
  
    /*
     * cursor at bottom of first sequence
     */
    y += charHeight - 1;
    evt = new MouseEvent(testee, Event.MOUSE_MOVE, 0L, 0, x, y, 0, 0, 0,
            false, 0);
    pos = testee.findMousePosition(evt);
    assertEquals(pos.seqIndex, 0);
    assertEquals(pos.annotationIndex, -1);
  
    /*
     * cursor at top of second sequence
     */
    y += 1;
    evt = new MouseEvent(testee, Event.MOUSE_MOVE, 0L, 0, x, y, 0, 0, 0,
            false, 0);
    pos = testee.findMousePosition(evt);
    assertEquals(pos.seqIndex, 1);
    assertEquals(pos.annotationIndex, -1);
  
    /*
     * cursor at bottom of second sequence
     */
    y += charHeight - 1;
    evt = new MouseEvent(testee, Event.MOUSE_MOVE, 0L, 0, x, y, 0, 0, 0,
            false, 0);
    pos = testee.findMousePosition(evt);
    assertEquals(pos.seqIndex, 1);
    assertEquals(pos.annotationIndex, -1);
  
    /*
     * cursor at bottom of last sequence
     * (scale + gap + sequences)
     */
    y = charHeight * (2 + alignmentHeight) - 1;
    evt = new MouseEvent(testee, Event.MOUSE_MOVE, 0L, 0, x, y, 0, 0, 0,
            false, 0);
    pos = testee.findMousePosition(evt);
    assertEquals(pos.seqIndex, alignmentHeight - 1);
    assertEquals(pos.annotationIndex, -1);
  
    /*
     * cursor below sequences, in 3-pixel gap above annotations
     */
    y += 1;
    evt = new MouseEvent(testee, Event.MOUSE_MOVE, 0L, 0, x, y, 0, 0, 0,
            false, 0);
    pos = testee.findMousePosition(evt);
    assertEquals(pos.seqIndex, alignmentHeight - 1);
    assertEquals(pos.annotationIndex, -1);
  
    /*
     * cursor still in the gap above annotations, now at the bottom of it
     * method reports index of nearest sequence above  
     */
    y += SeqCanvas.SEQS_ANNOTATION_GAP - 1; // 3-1 = 2
    evt = new MouseEvent(testee, Event.MOUSE_MOVE, 0L, 0, x, y, 0, 0, 0,
            false, 0);
    pos = testee.findMousePosition(evt);
    assertEquals(pos.seqIndex, alignmentHeight - 1);
    assertEquals(pos.annotationIndex, -1);
  
    /*
     * cursor at the top of the first annotation  
     */
    y += 1;
    evt = new MouseEvent(testee, Event.MOUSE_MOVE, 0L, 0, x, y, 0, 0, 0,
            false, 0);
    pos = testee.findMousePosition(evt);
    assertEquals(pos.seqIndex, alignmentHeight - 1);
    assertEquals(pos.annotationIndex, 0); // over first annotation
  
    /*
     * cursor at the bottom of the first annotation  
     */
    y += av.getAlignment().getAlignmentAnnotation()[0].height - 1;
    evt = new MouseEvent(testee, Event.MOUSE_MOVE, 0L, 0, x, y, 0, 0, 0,
            false, 0);
    pos = testee.findMousePosition(evt);
    assertEquals(pos.seqIndex, alignmentHeight - 1);
    assertEquals(pos.annotationIndex, 0);
  
    /*
     * cursor at the top of the second annotation  
     */
    y += 1;
    evt = new MouseEvent(testee, Event.MOUSE_MOVE, 0L, 0, x, y, 0, 0, 0,
            false, 0);
    pos = testee.findMousePosition(evt);
    assertEquals(pos.seqIndex, alignmentHeight - 1);
    assertEquals(pos.annotationIndex, 1);
  
    /*
     * cursor at the bottom of the second annotation  
     */
    y += av.getAlignment().getAlignmentAnnotation()[1].height - 1;
    evt = new MouseEvent(testee, Event.MOUSE_MOVE, 0L, 0, x, y, 0, 0, 0,
            false, 0);
    pos = testee.findMousePosition(evt);
    assertEquals(pos.seqIndex, alignmentHeight - 1);
    assertEquals(pos.annotationIndex, 1);
  
    /*
     * cursor at the top of the third annotation  
     */
    y += 1;
    evt = new MouseEvent(testee, Event.MOUSE_MOVE, 0L, 0, x, y, 0, 0, 0,
            false, 0);
    pos = testee.findMousePosition(evt);
    assertEquals(pos.seqIndex, alignmentHeight - 1);
    assertEquals(pos.annotationIndex, 2);
  
    /*
     * cursor at the bottom of the third annotation  
     */
    y += av.getAlignment().getAlignmentAnnotation()[2].height - 1;
    evt = new MouseEvent(testee, Event.MOUSE_MOVE, 0L, 0, x, y, 0, 0, 0,
            false, 0);
    pos = testee.findMousePosition(evt);
    assertEquals(pos.seqIndex, alignmentHeight - 1);
    assertEquals(pos.annotationIndex, 2);
  
    /*
     * cursor in gap between wrapped widths  
     */
    y += 1;
    evt = new MouseEvent(testee, Event.MOUSE_MOVE, 0L, 0, x, y, 0, 0, 0,
            false, 0);
    pos = testee.findMousePosition(evt);
    assertEquals(pos.seqIndex, -1);
    assertEquals(pos.annotationIndex, -1);
  
    /*
     * cursor at bottom of gap between wrapped widths  
     */
    y += charHeight - 1;
    evt = new MouseEvent(testee, Event.MOUSE_MOVE, 0L, 0, x, y, 0, 0, 0,
            false, 0);
    pos = testee.findMousePosition(evt);
    assertEquals(pos.seqIndex, -1);
    assertEquals(pos.annotationIndex, -1);
  
    /*
     * cursor at top of scale, second wrapped width  
     */
    y += 1;
    evt = new MouseEvent(testee, Event.MOUSE_MOVE, 0L, 0, x, y, 0, 0, 0,
            false, 0);
    pos = testee.findMousePosition(evt);
    assertEquals(pos.seqIndex, -1);
    assertEquals(pos.annotationIndex, -1);

    /*
     * cursor at bottom of scale, second wrapped width  
     */
    y += charHeight - 1;
    evt = new MouseEvent(testee, Event.MOUSE_MOVE, 0L, 0, x, y, 0, 0, 0,
            false, 0);
    pos = testee.findMousePosition(evt);
    assertEquals(pos.seqIndex, -1);
    assertEquals(pos.annotationIndex, -1);

    /*
     * cursor at top of first sequence, second wrapped width  
     */
    y += 1;
    evt = new MouseEvent(testee, Event.MOUSE_MOVE, 0L, 0, x, y, 0, 0, 0,
            false, 0);
    pos = testee.findMousePosition(evt);
    assertEquals(pos.seqIndex, 0);
    assertEquals(pos.annotationIndex, -1);
  }
  @BeforeClass(alwaysRun = true)
  public static void setUpBeforeClass() throws Exception
  {
    /*
     * use read-only test properties file
     */
    Cache.loadProperties("test/jalview/io/testProps.jvprops");
    Jalview.main(new String[] { "-nonews" });
  }
}